%% Created using Papers on Sun, 06 May 2018. %% http://papersapp.com/papers/ @article{Planque:2016et, author = {Planque, Benjamin}, title = {{Projecting the future state of marine ecosystems, {\textquotedblleft}la grande illusion{\textquotedblright}?}}, journal = {ICES J. Mar. Sci.}, year = {2016}, volume = {73}, number = {2}, pages = {204--208}, month = jan } @article{Thorpe:1983ca, author = {Thorpe, M F}, title = {{Continuous deformations in random networks}}, journal = {J Non-Cryst Solids}, year = {1983}, volume = {57}, number = {3}, pages = {355--370}, month = sep } @webpage{Anonymous:dwFkfejS, title = {{Boosting association rule mining in large datasets via Gibbs sampling}}, url = {http://www.pnas.org/content/113/18/4958.abstract.html?etoc} } @article{Delong:1988tf, author = {Delong, ER and Delong, DM and Clarke-Pearson, DI}, title = {{Comparing the areas under two or more correlated receiver operating characteristic curves: A nonparametric approach}}, journal = {Biometrics}, year = {1988}, volume = {44}, number = {3}, pages = {837--845} } @article{Novikov:ua, author = {Novikov, Dmitry S and Jensen, Jens H and Helpern, Joseph A and Fieremans, Els}, title = {{Revealing mesoscopic structural universality with diffusion}}, journal = {pnas.org} } @article{Barducci:2008ji, author = {Barducci, Alessandro and Bussi, Giovanni and Parrinello, Michele}, title = {{Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method}}, journal = {Phys. Rev. Lett.}, year = {2008}, volume = {100}, number = {2}, pages = {020603}, month = jan } @article{Pontiggia:2008up, author = {Pontiggia, F and Zen, A and Micheletti, C}, title = {{Small-and Large-Scale Conformational Changes of Adenylate Kinase: A Molecular Dynamics Study of the {\ldots}}}, journal = {Biophys. J.}, year = {2008} } @article{Rath:2012im, author = {Rath, Arianna and Deber, Charles M}, title = {{Protein Structure in Membrane Domains}}, journal = {Annu. Rev. Biophys.}, year = {2012}, volume = {41}, number = {1}, pages = {135--155}, month = jun } @article{Sakakibara:2009ec, author = {Sakakibara, Daisuke and Sasaki, Atsuko and Ikeya, Teppei and Hamatsu, Junpei and Hanashima, Tomomi and Mishima, Masaki and Yoshimasu, Masatoshi and Hayashi, Nobuhiro and Mikawa, Tsutomu and W{\"a}lchli, Markus and Smith, Brian O and Shirakawa, Masahiro and G{\"u}ntert, Peter and Ito, Yutaka}, title = {{Protein structure determination in living cells by in-cell NMR spectroscopy}}, journal = {Nature}, year = {2009}, volume = {458}, number = {7234}, pages = {102--105}, month = mar } @article{JIA:1994uq, author = {JIA, ZC and VANDONSELAAR, M and HENGSTENBERG, W and QUAIL, JW and DELBAERE, LTJ}, title = {{The 1-Center-Dot-6 Angstrom Structure of Histidine-Containing Phosphotransfer Protein Hpr From Streptococcus-Faecalis}}, journal = {J. Mol. Biol.}, year = {1994}, volume = {236}, number = {5}, pages = {1341--1355} } @article{Gaillard:2009gd, author = {Gaillard, Thomas and Dejaegere, Annick and Stote, Roland H}, title = {{Dynamics of $\beta$3 integrin I-like and hybrid domains: Insight from simulations on the mechanism of transition between open and closed forms}}, journal = {Proteins: Struct., Funct., Bioinf.}, year = {2009}, volume = {76}, number = {4}, pages = {977--994}, month = sep } @article{VanWynsberghe:2005ct, author = {Van Wynsberghe, Adam W and Cui, Qiang}, title = {{Comparison of mode analyses at different resolutions applied to nucleic acid systems.}}, journal = {Biophys. J.}, year = {2005}, volume = {89}, number = {5}, pages = {2939--2949} } @article{Lemmon:2008kt, author = {Lemmon, Mark A}, title = {{Membrane recognition by phospholipid-binding domains}}, journal = {Nat Rev Mol Cell Biol}, year = {2008}, volume = {9}, number = {2}, pages = {99--111}, month = feb } @article{Inanami:2014dh, author = {Inanami, T and Terada, T P and Sasai, M}, title = {{Folding pathway of a multidomain protein depends on its topology of domain connectivity}}, journal = {Proc. Natl. Acad. Sci. U. S. A.}, year = {2014}, volume = {111}, number = {45}, pages = {15969--15974}, month = nov } @article{VilaVicosa:2014ir, author = {Vila-Vi{\c c}osa, Diogo and Teixeira, Vitor H and Santos, Hugo A F and Baptista, Ant{\'o}nio M and Machuqueiro, Miguel}, title = {{Treatment of Ionic Strength in Biomolecular Simulations of Charged Lipid Bilayers}}, journal = {J Chem Theory Comput}, year = {2014}, pages = {141113160224002}, month = nov } @article{Southall:2002cc, author = {Southall, Noel T and Dill, Ken A and Haymet, A D J}, title = {{A View of the Hydrophobic Effect}}, journal = {J. Phys. Chem. B}, year = {2002}, volume = {106}, number = {3}, pages = {521--533}, month = jan } @article{Kneller:2012bxa, author = {Kneller, Gerald R and Hinsen, Konrad and Calligari, Paolo}, title = {{Communication: A minimal model for the diffusion-relaxation backbone dynamics of proteins}}, journal = {J. Chem. Phys.}, year = {2012}, volume = {136}, number = {19}, pages = {191101}, month = may } @article{Minton:2013jp, author = {Minton, Allen P}, title = {{QUANTITATIVE ASSESSMENT OF THE RELATIVE CONTRIBUTIONS OF STERIC REPULSION AND CHEMICAL INTERACTIONS TO MACROMOLECULAR CROWDING}}, journal = {Biopolymers}, year = {2013}, volume = {99}, number = {4}, pages = {239--244}, month = apr } @article{Bouvier:vi, author = {Bouvier, Guillaume and Desdouits, Nathan and Ferber, Mathias and Blondel, Arnaud and Nilges, Michael}, title = {{An automatic tool to analyze and cluster macromolecular conformations based on self-organizing maps}}, journal = {bioinformatics.oxfordjournals.org} } @article{Reuveni:uv, author = {Reuveni, Shlomi and Urbakh, Michael and Klafter, Joseph}, title = {{Role of substrate unbinding in Michaelis{\textendash}Menten enzymatic reactions}}, journal = {pnas.org} } @article{Bahar:2005bp, author = {Bahar, Ivet and Rader, A J}, title = {{Coarse-grained normal mode analysis in structural biology.}}, journal = {Current Opinion in Structural Biology}, year = {2005}, volume = {15}, number = {5}, pages = {586--592}, month = oct } @article{Kneller:2004dk, author = {Kneller, Gerald R and Hinsen, Konrad}, title = {{Fractional Brownian dynamics in proteins}}, journal = {J. Chem. Phys.}, year = {2004}, volume = {121}, number = {20}, pages = {10278--10283}, month = nov } @article{Baggerly:2009te, author = {Baggerly, K A and Coombes, K R}, title = {{JSTOR: The Annals of Applied Statistics, Vol. 3, No. 4 (December 2009), pp. 1309-1334}}, journal = {The Annals of Applied Statistics}, year = {2009} } @article{Phillips:2005ia, author = {Phillips, James C and Braun, Rosemary and Wang, Wei and Gumbart, James and Tajkhorshid, Emad and Villa, Elizabeth and Chipot, Christophe and Skeel, Robert D and Kal{\'e}, Laxmikant and Schulten, Klaus}, title = {{Scalable molecular dynamics with NAMD.}}, journal = {J. Comput. Chem.}, year = {2005}, volume = {26}, number = {16}, pages = {1781--1802}, month = nov } @article{Anonymous:hNmIuz9Q, title = {{Reference Manual for the 54 Mbps Wireless Router WGR614 v6}} } @article{Bianco:2015wr, author = {Bianco, V and Franzese, G}, title = {{Contribution of Water to Pressure and Cold Denaturation of Proteins}}, journal = {Phys. Rev. Lett.}, year = {2015} } @article{Hjermann:2004dn, author = {Hjermann, Dag {\O} and Stenseth, Nils Chr and Ottersen, Geir}, title = {{Indirect climatic forcing of the Barents Sea capelin: a cohort effect}}, journal = {Mar. Ecol. Prog. Ser.}, year = {2004}, volume = {273}, pages = {229--238}, month = jun } @article{Stirnemann:2014ca, author = {Stirnemann, Guillaume and Kang, Seung-gu and Zhou, Ruhong and Berne, Bruce J}, title = {{How force unfolding differs from chemical denaturation}}, journal = {Proc. Natl. Acad. Sci. U. S. A.}, year = {2014}, volume = {111}, number = {9}, pages = {3413--3418}, month = mar } @webpage{Anonymous:49hkAeIo, title = {{Membrane binding domains}}, url = {http://www.sciencedirect.com/science/article/pii/S1388198106000606} } @article{Fleming:2000hh, author = {Fleming, Patrick J and Richards, Frederic M}, title = {{Protein packing: dependence on protein size, secondary structure and amino acid composition}}, journal = {J. Mol. Biol.}, year = {2000}, volume = {299}, number = {2}, pages = {487--498}, month = jun } @webpage{Case:ws, author = {Case, David A}, title = {{NMR Refinement}}, url = {http://www.wiley.com/legacy/wileychi/ecc/samples/sample09.pdf} } @article{deBruyn:2001im, author = {deBruyn, AMH and Meeuwigg, J J}, title = {{Detecting lunar cycles in marine ecology: periodic regression versus categorical ANOVA}}, journal = {Mar. Ecol. Prog. Ser.}, year = {2001}, volume = {214}, pages = {307--310} } @article{Thennarasu:2005jw, author = {Thennarasu, Sathiah and Lee, Dong-Kuk and Poon, Alan and Kawulka, Karen E and Vederas, John C and Ramamoorthy, Ayyalusamy}, title = {{Membrane permeabilization, orientation, and antimicrobial mechanism of subtilosin A.}}, journal = {Chemistry and Physics of Lipids}, year = {2005}, volume = {137}, number = {1-2}, pages = {38--51}, month = oct } @webpage{Anonymous:Z1KYaLK7, title = {{Dissecting the Hydrophobic Effect on the Molecular Level: The Role of Water, Enthalpy, and Entropy in Ligand Binding to Thermolysin - Biela - 2013 - Angewandte Chemie International Edition - Wiley Online Library}}, url = {http://onlinelibrary.wiley.com/doi/10.1002/anie.201208561/full} } @article{Sing:2005jf, author = {Sing, Tobias and Sander, Oliver and Beerenwinkel, Niko and Lengauer, Thomas}, title = {{ROCR: visualizing classifier performance in R}}, journal = {Bioinformatics}, year = {2005}, volume = {21}, number = {20}, pages = {3940}, month = oct } @article{Anonymous:766elNek, author = {Zheng, Fan and Zhang, Jian and Grigoryan, Gevorg}, title = {{Tertiary Structural Propensities Reveal Fundamental Sequence/Structure Relationships}}, journal = {Structure}, year = {2015}, volume = {23}, number = {5}, pages = {961--971}, month = may } @article{MURZIN:1995uha, author = {Murzin, Alexey G and Brenner, Steven E. and Hubbard, Tim and Chothia, Cyrus}, title = {{SCOP - A structural classification of proteins. Database for the investigation of sequences and structures}}, journal = {J. Mol. Biol.}, year = {1995}, volume = {247}, number = {4}, pages = {536--540} } @article{Schiffer:1992ws, author = {Schiffer, M and Chang, C H and Stevens, F J}, title = {{The functions of tryptophan residues in membrane proteins.}}, journal = {Protein Eng.}, year = {1992}, volume = {5}, number = {3}, pages = {213--214}, month = apr } @article{Dixit:2018by, author = {Dixit, Purushottam D and Wagoner, Jason and Weistuch, Corey and Press{\'e}, Steve and Ghosh, Kingshuk and Dill, Ken A}, title = {{Perspective: Maximum caliber is a general variational principle for dynamical systems}}, journal = {J. Chem. Phys.}, year = {2018}, volume = {148}, number = {1}, pages = {010901}, month = jan } @article{Anonymous:wFzBG1_h, author = {Freedman, David}, title = {{Some issues n the foundation of statistics}}, year = {1994}, pages = {30}, month = sep } @article{Hessa:2005hr, author = {Hessa, T}, title = {{Membrane Insertion of a Potassium-Channel Voltage Sensor}}, journal = {Science}, year = {2005}, volume = {307}, number = {5714}, pages = {1427--1427}, month = mar } @article{Bose:1936ta, author = {Bose, Raj Chandra}, title = {{On the Exact Distribution and Moment-Coefficients of the D{\texttwosuperior}-Statistic}}, journal = {Sankhy{\=a}: The Indian Journal of Statistics (1933-1960)}, year = {1936}, volume = {2}, number = {2}, pages = {143--154}, month = jan } @article{Conway:2009wk, author = {Conway, John H and Kochen, Simon}, title = {{The Strong Free Will Theorem}}, year = {2009}, pages = {1--7}, month = dec } @article{Gamsjaeger:2005jd, author = {Gamsjaeger, Roland and Johs, Alexander and Gries, Anna and Gruber, Hermann J and Romanin, Christoph and Prassl, Ruth and Hinterdorfer, Peter}, title = {{Membrane binding of $\beta$ 2-glycoprotein I can be described by a two-state reaction model: an atomic force microscopy and surface plasmon resonance study}}, journal = {Biochem J}, year = {2005}, volume = {389}, number = {3}, pages = {665--673}, month = aug } @article{Anonymous:Zd4yw6DP, title = {{Kvantemekanikk - kompendie 1 - 2}}, year = {2005}, pages = {1--43}, month = sep } @article{Kurylowicz:2010gt, author = {Kurylowicz, Martin and Yu, Ching-Hsing and Pom{\`e}s, R{\'e}gis}, title = {{Systematic Study of Anharmonic Features in a Principal Component Analysis of Gramicidin A}}, journal = {Biophys. J.}, year = {2010}, volume = {98}, number = {3}, pages = {386--395}, month = feb } @article{:2017um, author = {23, Sci Publ Svcs Chennai India 4507 2000 Jan 05 15 06}, title = {{Beyond subjective and objective in statistics}}, year = {2017}, pages = {1--31}, month = feb } @article{Hensen:2012fx, author = {Hensen, Ulf and Meyer, Tim and Haas, J{\"u}rgen and Rex, Ren{\'e} and Vriend, Gert and Grubm{\"u}ller, Helmut}, title = {{Exploring protein dynamics space: the dynasome as the missing link between protein structure and function.}}, journal = {PLoS ONE}, year = {2012}, volume = {7}, number = {5}, pages = {e33931} } @article{Segers:2007df, author = {Segers, K and Sperandio, O and Sack, M and Fischer, R and Miteva, M A and Rosing, J and Nicolaes, G A F and Villoutreix, B O}, title = {{Design of protein membrane interaction inhibitors by virtual ligand screening, proof of concept with the C2 domain of factor V}}, journal = {Proc. Natl. Acad. Sci. U. S. A.}, year = {2007}, volume = {104}, number = {31}, pages = {12697--12702}, month = jul } @article{Kumar:2014jy, author = {Kumar, Rajendra and Grubm{\"u}ller, Helmut}, title = {{Elastic Properties and Heterogeneous Stiffness of the Phi29 Motor Connector Channel}}, journal = {Biophys. J.}, year = {2014}, volume = {106}, number = {6}, pages = {1338--1348}, month = mar } @article{HOLM:1998um, author = {HOLM, L and SANDER, C}, title = {{Touring protein fold space with Dali/FSSP}}, journal = {Nucleic Acids Res.}, year = {1998}, volume = {26}, number = {1}, pages = {316--319} } @article{Evans:2015tva, author = {Evans, Robert and Wilding, Nigel B}, title = {{Quantifying Density Fluctuations in Water at a Hydrophobic Surface: Evidence for Critical Drying.}}, journal = {Phys. Rev. Lett.}, year = {2015}, volume = {115}, number = {1}, pages = {016103}, month = jul } @article{Yamato:1993bv, author = {Yamato, T and Higo, J and Seno, Y and GO, N}, title = {{Conformational deformation in deoxymyoglobin by hydrostatic pressure.}}, journal = {Proteins: Struct., Funct., Bioinf.}, year = {1993}, volume = {16}, number = {4}, pages = {327--340}, month = aug } @article{Hilser:2012em, author = {Hilser, Vincent J and Wrabl, James O and Motlagh, Hesam N}, title = {{Structural and Energetic Basis of Allostery}}, journal = {Annu. Rev. Biophys.}, year = {2012}, volume = {41}, number = {1}, pages = {585--609}, month = jun } @article{Resh:1993ff, author = {Resh, M}, title = {{Interaction of tyrosine kinase oncoproteins with cellular membranes}}, journal = {Biochimica et Biophysica Acta (BBA) - Reviews on Cancer}, year = {1993}, volume = {1155}, number = {3}, pages = {307--322}, month = dec } @article{Cooper:2010jw, author = {Cooper, Seth and Khatib, Firas and Treuille, Adrien and Barbero, Janos and Lee, Jeehyung and Beenen, Michael and Leaver-Fay, Andrew and Baker, David and Popovi{\'c}, Zoran and Players, Foldit}, title = {{Predicting protein structures with a multiplayer online game}}, journal = {Nature}, year = {2010}, volume = {466}, number = {7307}, pages = {756--760}, month = may } @article{Gjosaeter:1999us, author = {Gjosaeter, H}, title = {{Studies on the Barents Sea capelin (Mallotus villosus M{\"u}ller)}}, year = {1999} } @techreport{Anonymous:iFEYAjb-, title = {{Microsoft Word - Bycatch of harbour porpoise, harbour seal and grey seal in Norwegian gillnet fisheries .docx}}, year = {2016}, month = oct } @article{Gregry:2009wy, author = {Gregry, T Ryan}, title = {{Understanding Natural Selection: Essential Concepts and Common Misconsceptions}}, year = {2009}, pages = {1--37}, month = aug } @article{Hinsen:2016vy, author = {Hinsen, Konrad}, title = {{Scientific notations for the digital era}}, year = {2016}, month = may } @article{Boomsma:2008kp, author = {Boomsma, W and Mardia, K V and Taylor, C C and Ferkinghoff-Borg, J and Krogh, A and Hamelryck, T}, title = {{A generative, probabilistic model of local protein structure}}, journal = {Proc. Natl. Acad. Sci. U. S. A.}, year = {2008}, volume = {105}, number = {26}, pages = {8932--8937}, month = jul } @article{Stahelin:uj, author = {Stahelin, Robert V and Long, Fei and Diraviyam, Karthikeyan and Bruzik, Karol S and Murray, Diana and Cho, Wonhwa}, title = {{Phosphatidylinositol 3-Phosphate Induces the Membrane Penetration of the FYVE Domains of Vps27p and Hrs}}, journal = {J. Biol. Chem.}, year = {2002}, volume = {277}, number = {29}, pages = {26379--26388}, month = jul } @article{Aittokallio:2006hf, author = {Aittokallio, T}, title = {{Graph-based methods for analysing networks in cell biology}}, journal = {Brief. Bioinformatics}, year = {2006}, volume = {7}, number = {3}, pages = {243--255}, month = may } @article{Katzenellenbogen:1997vo, author = {Katzenellenbogen, B S and Montano, M M and Ekena, K}, title = {{Antiestrogens: Mechanisms of action and resistance in breast cancer - Springer}}, journal = {Breast cancer research {\ldots}}, year = {1997} } @article{Broemstrup:2010fu, author = {Broemstrup, Torben and Reuter, Nathalie}, title = {{How does Proteinase 3 interact with lipid bilayers? }}, journal = {Phys. Chem. Chem. Phys.}, year = {2010}, volume = {12}, number = {27}, pages = {7487--7496} } @article{Adelman:2010eq, author = {Adelman, Joshua L and Chodera, John D and Kuo, I-Feng W and Miller III, Thomas F and Barsky, Daniel}, title = {{The Mechanical Properties of PCNA: Implications for the Loading and Function of a DNA Sliding Clamp}}, journal = {Biophys. J.}, year = {2010}, volume = {98}, number = {12}, pages = {3062--3069}, month = jun } @webpage{Anonymous:vO03VgvL, title = {{PLOS Computational Biology: ECOD: An Evolutionary Classification of Protein Domains}}, url = {http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003926} } @article{Ortiz:2002ic, author = {Ortiz, AR and Strauss, CEM and Olmea, O}, title = {{MAMMOTH (Matching molecular models obtained from theory): An automated method for model comparison}}, journal = {Protein Sci.}, year = {2002}, volume = {11}, number = {11}, pages = {2606--2621} } @article{Taylor:2006ks, author = {Taylor, WR}, title = {{Decoy models for protein structure comparison score normalisation}}, journal = {J. Mol. Biol.}, year = {2006}, volume = {357}, number = {2}, pages = {676--699} } @article{Collins:2011wc, author = {Collins, Cody}, title = {{Starcraft 2 Season 3 1v1 Ladder Map Strategies}}, year = {2011}, pages = {1--78}, month = sep } @article{Matheron:1973tn, author = {Matheron, G}, title = {{The Intrinsic Random Functions and Their Applications}}, journal = {Advances in Applied Probability}, year = {1973}, volume = {5}, number = {3}, pages = {439--468}, month = dec } @article{PascualGarca:2009tk, author = {Pascual-Garc{\'\i}a, Alberto and Abia, David and Ortiz, Angel R and Bastolla, Ugo}, title = {{Cross-over between discrete and continuous protein structure space: insights into automatic classification and networks of protein structures.}}, journal = {PLoS Comput. Biol.}, year = {2009}, volume = {5}, number = {3}, pages = {e1000331}, month = mar } @article{Leek:tj, author = {Leek, Jeffrey T and Peng, Roger D}, title = {{Opinion: Reproducible research can still be wrong: Adopting a prevention approach}}, journal = {pnas.org} } @article{Lezon:2011ve, author = {Lezon, TR}, title = {{The effects of rigid motions on elastic network model force constants - Lezon - 2012 - Proteins: Structure, Function, and Bioinformatics - Wiley Online Library}}, journal = {Proteins: Structure}, year = {2011} } @article{Jacobs:2001we, author = {Jacobs, DJ and Rader, AJ and Kuhn, LA and Thorpe, MF}, title = {{Protein flexibility predictions using graph theory}}, year = {2001}, volume = {44}, number = {2}, pages = {150--165} } @article{Jacobs:2010jt, author = {Jacobs, Donald J}, title = {{Ensemble-based methods for describing protein dynamics.}}, journal = {Curr Opin Pharmacol}, year = {2010}, volume = {10}, number = {6}, pages = {760--769}, month = dec } @article{vanMeer:2008gi, author = {van Meer, Gerrit and Voelker, Dennis R and Feigenson, Gerald W}, title = {{Membrane lipids: where they are and how they behave}}, journal = {Nat Rev Mol Cell Biol}, year = {2008}, volume = {9}, number = {2}, pages = {112--124}, month = feb } @webpage{NCIUBMB:vka, author = {{NC-IUBMB}}, title = {{Enzyme nomenclature - recommendations of the nomenclature committee of the international union of biochemistry and molecular biology on the nomenclature and classification of enzymes by the reactions they catalyse}}, year = {2011}, month = dec, url = {http://www.chem.qmul.ac.uk/iubmb/enzyme/} } @article{Lijnzaad:2008hg, author = {Lijnzaad, Philip and Feenstra, K. Anton and Heringa, Jaap and Holstege, Frank C P}, title = {{On defining the dynamics of hydrophobic patches on protein surfaces}}, journal = {Proteins: Struct., Funct., Bioinf.}, year = {2008}, volume = {72}, number = {1}, pages = {105--114}, month = jan } @article{Soheilifard:2008kp, author = {Soheilifard, Reza and Makarov, Dmitrii E and Rodin, Gregory J}, title = {{Critical evaluation of simple network models of protein dynamics and their comparison with crystallographic B-factors}}, journal = {Phys. Biol.}, year = {2008}, volume = {5}, number = {2}, pages = {026008}, month = jun } @article{Aloulou:2012vf, author = {Aloulou, Ahmed and Ali, Yassine Ben and Bezzine, Sofiane and Gargouri, Youssef and Gelb, Michael H}, title = {{Phospholipases: an overview}}, year = {2012}, pages = {63--85} } @article{Remsing:wz, author = {Remsing, Richard C and Liu, Shule and Weeks, John D}, title = {{Long-ranged contributions to solvation free energies from theory and short-ranged models}}, journal = {pnas.org} } @article{Zhou:2006hz, author = {Zhou, S K and Chellappa, R}, title = {{From sample similarity to ensemble similarity: probabilistic distance measures in reproducing kernel Hilbert space}}, journal = {IEEE Trans. Pattern Anal. Machine Intell.}, year = {2006}, volume = {28}, number = {6}, pages = {917--929} } @article{Javanmard:tp, author = {Javanmard, Adel and Montanari, Andrea and Ricci-Tersenghi, Federico}, title = {{Phase transitions in semidefinite relaxations}}, journal = {pnas.org} } @article{Lomize:2011gj, author = {Lomize, Andrei L and Pogozheva, Irina D and Mosberg, Henry I}, title = {{Anisotropic solvent model of the lipid bilayer. 2. Energetics of insertion of small molecules, peptides, and proteins in membranes.}}, journal = {J Chem Inf Model}, year = {2011}, volume = {51}, number = {4}, pages = {930--946}, month = apr } @article{Duckworth:UTlkxIyo, author = {Duckworth, Angela L and Seligman, Martin EP}, title = {{Self-Discipline Outdoes IQ in Predicting Academic Performance of Adolescents}} } @article{Lomize:2007gm, author = {Lomize, Andrei L and Pogozheva, Irina D and Lomize, Mikhail A and Mosberg, Henry I}, title = {{The role of hydrophobic interactions in positioning of peripheral proteins in membranes}}, journal = {BMC Structural Biology}, year = {2007}, volume = {7}, pages = {44} } @webpage{Anonymous:lyh41a9V, title = {{SPECTRUS: A Dimensionality Reduction Approach for Identifying Dynamical Domains in Protein Complexes from Limited Structural Datasets}}, url = {http://www.sciencedirect.com/science/article/pii/S0969212615002270} } @article{Plouffe:2000ux, author = {Plouffe, Knuth Graham Patashnik Simon}, title = {{Concrete Mathematics}}, year = {2000}, pages = {1--639}, month = sep } @article{College:2003vk, author = {College, Colby}, title = {{NormalModesText}}, year = {2003}, pages = {1--13}, month = feb } @webpage{Anonymous:TGaP-x0y, title = {{la502115g}}, url = {http://pubs.acs.org/doi/pdf/10.1021/la502115g} } @article{Isas:2004fw, author = {Isas, J M and Langen, R and Hubbell, W L and Haigler, H T}, title = {{Structure and Dynamics of a Helical Hairpin that Mediates Calcium-dependent Membrane Binding of Annexin B12}}, journal = {J. Biol. Chem.}, year = {2004}, volume = {279}, number = {31}, pages = {32492--32498}, month = jul } @article{Blaser:2009wp, author = {Blaser, G and Sanderson, J M and Wilson, M R}, title = {{Free-energy relationships for the interactions of tryptophan with phosphocholines - Organic {\&} Biomolecular Chemistry (RSC Publishing) DOI:10.1039/B913919B}}, journal = {Organic {\&} Biomolecular {\ldots}}, year = {2009} } @article{Liberles:2012bi, author = {Liberles, David A and Teichmann, Sarah A and Bahar, Ivet and Bastolla, Ugo and Bloom, Jesse and Bornberg-Bauer, Erich and Colwell, Lucy J and de Koning, A P Jason and Dokholyan, Nikolay V and Echave, Juli{\'a}n and Elofsson, Arne and Gerloff, Dietlind L and Goldstein, Richard A and Grahnen, Johan A and Holder, Mark T and Lakner, Clemens and Lartillot, Nicholas and Lovell, Simon C and Naylor, Gavin and Perica, Tina and Pollock, David D and Pupko, Tal and Regan, Lynne and Roger, Andrew and Rubinstein, Nimrod and Shakhnovich, Eugene and Sj{\"o}lander, Kimmen and Sunyaev, Shamil and Teufel, Ashley I and Thorne, Jeffrey L and Thornton, Joseph W and Weinreich, Daniel M and Whelan, Simon}, title = {{REVIEWS: The interface of protein structure, protein biophysics, and molecular evolution - author proof}}, journal = {Proteins: Struct., Funct., Bioinf.}, year = {2012}, month = jun } @article{Siglioccolo:2010if, author = {Siglioccolo, Alessandro and Gerace, Raffaele and Pascarella, Stefano}, title = {{``Cold spots'' in protein cold adaptation: Insights from normalized atomic displacement parameters (B{\textasciiacute}-factors)}}, journal = {Biophys. Chem.}, year = {2010}, volume = {153}, number = {1}, pages = {104--114} } @article{Anonymous:TBB8RLj2, title = {{ERGObaby carrier - manual}}, year = {2010}, pages = {1--3}, month = oct } @article{Hinsen:2006es, author = {Hinsen, Konrad}, title = {{Comment on: {\textquotedblleft}Energy landscape of a small peptide revealed by dihedral angle principal component analysis{\textquotedblright}}}, journal = {Proteins: Struct., Funct., Bioinf.}, year = {2006}, volume = {64}, number = {3}, pages = {795--797}, month = feb } @article{Dziubinski:wr, author = {Dziubi{\'{n}}ski, Maciej and Daniluk, Pawe{\l} and Lesyng, Bogdan}, title = {{ResiCon: a method for the identification of dynamic domains, hinges and interfacial regions in proteins}}, journal = {bioinformatics.oxfordjournals.org} } @article{group:2006to, author = {group, Luthey-Schulten}, title = {{Evolution of Biomolecular Structure }}, year = {2006}, pages = {1--46}, month = sep } @article{Ulmschneider:2007fa, author = {Ulmschneider, Martin B and Ulmschneider, Jakob P and Sansom, Mark S P and Di Nola, Alfredo}, title = {{A Generalized Born Implicit-Membrane Representation Compared to Experimental Insertion Free Energies}}, journal = {Biophys. J.}, year = {2007}, volume = {92}, number = {7}, pages = {2338--2349}, month = apr } @article{Wei:1989ka, author = {Wei, Gaoyuan}, title = {{Distribution function of the radius of gyration for Gaussian molecules}}, journal = {J. Chem. Phys.}, year = {1989}, volume = {90}, number = {10}, pages = {5873} } @article{Sharpe:2010wy, author = {Sharpe, H J and Stevens, T J and Munro, S}, title = {{ScienceDirect.com - Cell - A Comprehensive Comparison of Transmembrane Domains Reveals Organelle-Specific Properties}}, journal = {Cell}, year = {2010} } @article{Johansson:2006er, author = {Johansson, Anna C V and Lindahl, Erik}, title = {{Amino-Acid Solvation Structure in Transmembrane Helices from Molecular Dynamics Simulations}}, journal = {Biophys. J.}, year = {2006}, volume = {91}, number = {12}, pages = {4450--4463}, month = dec } @article{Zhang:1995vz, author = {Zhang, G and Kazanietz, M G and Blumberg, P M and Hurley, J H}, title = {{Crystal structure of the cys2 activator-binding domain of protein kinase C delta in complex with phorbol ester.}}, journal = {Cell}, year = {1995}, volume = {81}, number = {6}, pages = {917--924}, month = jun } @article{Haliloglu:1997uy, author = {Haliloglu, Turkan and Bahar, Ivet and Erman, Burak}, title = {{Gaussian Dynamics of Folded Proteins}}, journal = {Phys. Rev. Lett.}, year = {1997}, volume = {79}, number = {16}, pages = {3090--3093}, month = oct } @article{Das:2014fm, author = {Das, Joydip and Rahman, Ghazi M}, title = {{C1 Domains: Structure and Ligand-Binding Properties}}, journal = {Chem. Rev}, year = {2014}, pages = {141106102517006}, month = nov } @webpage{Tao:BWRa_muU, author = {Tao, Terence}, title = {{An introduction ot measure theory}}, url = {http://www.faculty.jacobs-university.de/poswald/teaching/RealAnal2/handouts/TaoMeasureTheory.pdf} } @article{Gjosaeter:1999wu, author = {Gjosaeter, H and Dalpadado, P and Hassel, A}, title = {{GROWTH OF THE BARENTS SEA CAPELIN (MALLOTUS VILLOSUS M{\"U}LLER) III}}, journal = {STUDIES ON THE {\ldots}}, year = {1999} } @article{Fuglebakk:2013hh, author = {Fuglebakk, Edvin and Reuter, Nathalie and Hinsen, Konrad}, title = {{Evaluation of Protein Elastic Network Models Based on an Analysis of Collective Motions}}, journal = {J Chem Theory Comput}, year = {2013}, month = nov } @article{epitoolsEpidemiolo:dQp6gsqn, author = {Aragon, Tomas}, title = {{epitools: Epidemiology Tools. R package}} } @article{Kiel:2008dv, author = {Kiel, Christina and Beltrao, Pedro and Serrano, Luis}, title = {{Analyzing protein interaction networks using structural information}}, journal = {Annu Rev Biochem}, year = {2008}, volume = {77}, pages = {415--441} } @article{Maddy:2008hf, author = {Maddy, Penelope}, title = {{HOW APPLIED MATHEMATICS BECAME PURE}}, journal = {Review of Symbolic Logic}, year = {2008}, volume = {1}, number = {01}, pages = {1--26}, month = jun } @article{Parisi:2005je, author = {Parisi, G and Echave, J}, title = {{Generality of the Structurally Constrained Protein Evolution model: assessment on representatives of the four main fold classes}}, journal = {Gene}, year = {2005}, volume = {345}, number = {1}, pages = {45--53}, month = jan } @incollection{Carnevale:2010ku, author = {Carnevale, Vincenzo and Micheletti, Cristian and Pontiggia, Francesco and Potestio, Raffaello}, title = {{Bridging the Atomic and Coarse-Grained Descriptions of Collective Motions in Proteins}}, booktitle = {apps.webofknowledge.com}, year = {2010}, pages = {159--178}, publisher = {Springer New York}, address = {New York, NY}, month = sep } @article{Samish:2014ev, author = {Samish, I and Bourne, P E and Najmanovich, R J}, title = {{Achievements and challenges in structural bioinformatics and computational biophysics}}, journal = {Bioinformatics}, year = {2014}, month = dec } @article{Harder:2010ea, author = {Harder, Tim and Boomsma, Wouter and Paluszewski, Martin and Frellsen, Jes and Johansson, Kristoffer E and Hamelryck, Thomas}, title = {{Beyond rotamers: a generative, probabilistic model of side chains in proteins.}}, journal = {BMC Bioinformatics}, year = {2010}, volume = {11}, pages = {306} } @article{Fober:2009io, author = {Fober, T and Mernberger, M and Klebe, G and Hullermeier, E}, title = {{Evolutionary construction of multiple graph alignments for the structural analysis of biomolecules}}, journal = {Bioinformatics}, year = {2009}, volume = {25}, number = {16}, pages = {2110--2117}, month = aug } @article{vanAnders:tv, author = {van Anders, Greg and Klotsa, Daphne and Ahmed, N Khalid and Engel, Michael and Glotzer, Sharon C}, title = {{Understanding shape entropy through local dense packing}}, journal = {pnas.org} } @techreport{Bernstein:2011vw, author = {Bernstein, Jeffrey}, title = {{FIVE STEPS TO JEALOUSY.doc}}, year = {2011}, month = jul } @article{Bakrac:2008fy, author = {Bakrac, B and Gutierrez-Aguirre, I and Podlesek, Z and Sonnen, A F P and Gilbert, R J C and Macek, P and Lakey, J H and Anderluh, G}, title = {{Molecular Determinants of Sphingomyelin Specificity of a Eukaryotic Pore-forming Toxin}}, journal = {J. Biol. Chem.}, year = {2008}, volume = {283}, number = {27}, pages = {18665--18677}, month = may } @article{Emperador:2008fn, author = {Emperador, Agusti and Carrillo, Oliver and Rueda, Manuel and Orozco, Modesto}, title = {{Exploring the suitability of coarse-grained techniques for the representation of protein dynamics}}, journal = {Biophys. J.}, year = {2008}, volume = {95}, number = {5}, pages = {2127--2138} } @article{Noy:2007cl, author = {Noy, Agnes and Perez, Alberto and Laughton, Charles A and Orozco, Modesto}, title = {{Theoretical study of large conformational transitions in DNA: the B A conformational change in water and ethanol/water}}, journal = {Nucleic Acids Res.}, year = {2007}, volume = {35}, number = {10}, pages = {3330--3338} } @webpage{Anonymous:YLcyF90e, title = {{Increased Reliability of Nuclear Magnetic Resonance Protein Structures by Consensus Structure Bundles: Structure}}, url = {http://www.cell.com/structure/abstract/S0969-2126(14)00408-0} } @article{Merritt:1999up, author = {Merritt, EA}, title = {{Comparing anisotropic displacement parameters in protein structures}}, journal = {Acta Crystallogr D}, year = {1999}, volume = {55}, pages = {1997--2004} } @article{Jian:2015do, author = {Jian, Xiaoying and Tang, Wai-Kwan and Zhai, Peng and Roy, Neeladri Sekhar and Luo, Ruibai and Gruschus, James M and Yohe, Marielle E and Chen, Pei-Wen and Li, Yifei and Byrd, R Andrew and Xia, Di and Randazzo, Paul A}, title = {{Molecular Basis for Cooperative Binding of Anionic Phospholipids to the PH Domain of the Arf GAP ASAP1}}, journal = {Structure}, year = {2015}, volume = {23}, number = {11}, pages = {1977--1988}, month = nov } @inproceedings{Carnevale:2007do, author = {Carnevale, Vincenzo and Pontiggia, Francesco and Micheletti, Cristian}, title = {{Structural and dynamical alignment of enzymes with partial structural similarity}}, booktitle = {J Phys-Condens Mat}, year = {2007}, pages = {285206(14)} } @article{Kucerka:2008il, author = {Ku{\v c}erka, Norbert and Nagle, John F and Sachs, Jonathan N and Feller, Scott E and Pencer, Jeremy and Jackson, Andrew and Katsaras, John}, title = {{Lipid Bilayer Structure Determined by the Simultaneous Analysis of Neutron and X-Ray Scattering Data}}, journal = {Biophys. J.}, year = {2008}, volume = {95}, number = {5}, pages = {2356--2367}, month = sep } @article{Cheng:2015ir, author = {Cheng, Yifan}, title = {{Single-Particle Cryo-EM at Crystallographic Resolution}}, journal = {Cell}, year = {2015}, volume = {161}, number = {3}, pages = {450--457}, month = apr } @article{Hilser:1996ft, author = {Hilser, V J and Freire, E}, title = {{Structure-based calculation of the equilibrium folding pathway of proteins. Correlation with hydrogen exchange protection factors.}}, journal = {J. Mol. Biol.}, year = {1996}, volume = {262}, number = {5}, pages = {756--772}, month = oct } @article{Hess:1997ug, author = {Hess, B and Bekker, H and Berendsen, H J C and Fraaije, J G E M}, title = {{LINCS: a linear constraint solver for molecular simulations}}, journal = {J. Comput. Chem.}, year = {1997}, volume = {18}, number = {12}, pages = {1463--1472} } @article{Kristensen:2015wk, author = {Kristensen, Kasper and Nielsen, Anders and Berg, Casper W and Skaug, Hans and Bell, Brad}, title = {{TMB: Automatic Differentiation and Laplace Approximation}}, year = {2015}, eprint = {1509.00660}, eprinttype = {arxiv}, month = sep } @article{Anonymous:kYS1rPLA, title = {{Structural_Testing_1}}, year = {1998}, pages = {49} } @article{Mason:2002tb, author = {Mason, SJ and Graham, NE}, title = {{Areas beneath the relative operating characteristics (ROC) and relative operating levels (ROL) curves: Statistical significance and interpretation}}, journal = {Q J Roy Meteor Soc}, year = {2002}, volume = {128}, number = {584}, pages = {2145--2166} } @article{Manning:2008ei, author = {Manning, Jonathan R and Jefferson, Emily R and Barton, Geoffrey J}, title = {{The contrasting properties of conservation and correlated phylogeny in protein functional residue prediction}}, journal = {BMC Bioinformatics}, year = {2008}, volume = {9}, pages = {51} } @article{Hinsen:2008fk, author = {Hinsen, Konrad and Kneller, Gerald R}, title = {{Solvent effects in the slow dynamics of proteins}}, journal = {Proteins: Struct., Funct., Bioinf.}, year = {2008}, volume = {70}, number = {4}, pages = {1235--1242} } @article{Reichheld:2009tz, author = {Reichheld, Sean E and Yu, Zhou and Davidson, Alan R}, title = {{The induction of folding cooperativity by ligand binding drives the allosteric response of tetracycline repressor}}, journal = {Proceedings of the {\ldots}}, year = {2009} } @article{Lu:2008hn, author = {Lu, Chih-Hao and Huang, Shao-Wei and Lai, Yan-Long and Lin, Chih-Peng and Shih, Chien-Hua and Huang, Cuen-Chao and Hsu, Wei-Lun and Hwang, Jenn-Kang}, title = {{On the relationship between the protein structure and protein dynamics}}, journal = {Proteins: Struct., Funct., Bioinf.}, year = {2008}, volume = {72}, number = {2}, pages = {625--634}, month = feb } @article{White:aknzxSGL, author = {White, Stephen H}, title = {{Membrane Protein Insertion: The Biology{\textendash}Physics Nexus}}, journal = {jgp.rupress.org} } @article{Gjosaeter:1999vr, author = {Gjosaeter, H}, title = {{GROWTH OF THE BARENTS SEA CAPELIN (MALLOTUS VILLOSUS M{\"U}LLER) II}}, journal = {STUDIES ON THE BARENTS SEA CAPELIN ( {\ldots}}, year = {1999} } @webpage{Lomize:uv, author = {Lomize, A and Lomize, M and Pogozheva, I}, title = {{Online documentation for OPM}}, url = {http://opm.phar.umich.edu} } @article{Carpena:2009dx, author = {Carpena, P and Bernaola-Galv{\'a}n, P and Hackenberg, M and Coronado, A V and Oliver, J L}, title = {{Level statistics of words: Finding keywords in literary texts and symbolic sequences}}, journal = {Phys. Rev. E}, year = {2009}, volume = {79}, number = {3}, month = mar } @article{Geladi:1986cy, author = {Geladi, P}, title = {{Partial least-squares regression: a tutorial}}, journal = {Analytica Chimica Acta}, year = {1986}, volume = {185}, number = {1}, pages = {1--17} } @article{Hand:2009gu, author = {Hand, David J.}, title = {{Measuring classifier performance: a coherent alternative to the area under the ROC curve}}, journal = {Machine Learning}, year = {2009}, volume = {77}, number = {1}, pages = {103--123} } @article{Grishin:2001ks, author = {Grishin, NV}, title = {{Fold change in evolution of protein structures}}, journal = {Journal of structural biology}, year = {2001}, volume = {134}, pages = {167--185} } @article{Chandler:2005ds, author = {Chandler, David}, title = {{Interfaces and the driving force of hydrophobic assembly}}, journal = {Nature}, year = {2005}, volume = {437}, number = {7059}, pages = {640--647}, month = sep } @article{Perticaroli:2014by, author = {Perticaroli, Stefania and Nickels, Jonathan D and Ehlers, Georg and Sokolov, Alexei P}, title = {{Rigidity, Secondary Structure, and the Universality of the Boson Peak in Proteins}}, journal = {Biophys. J.}, year = {2014}, volume = {106}, number = {12}, pages = {2667--2674}, month = jun } @article{Defante:2015bi, author = {Defante, Adrian P and Burai, Tarak N and Becker, Matthew L and Dhinojwala, Ali}, title = {{Consequences of Water between Two Hydrophobic Surfaces on Adhesion and Wetting}}, journal = {Langmuir}, year = {2015}, volume = {31}, number = {8}, pages = {2398--2406}, month = mar } @article{Koldso:2014je, author = {Kolds{\o}, Heidi and Shorthouse, David and H{\'e}lie, Jean and Sansom, Mark S P}, title = {{Lipid clustering correlates with membrane curvature as revealed by molecular simulations of complex lipid bilayers.}}, journal = {PLoS Comput. Biol.}, year = {2014}, volume = {10}, number = {10}, pages = {e1003911}, month = oct } @article{Dalpadado:2014ib, author = {Dalpadado, Padmini and Arrigo, Kevin R and Hj{\o}llo, Solfrid S and Rey, Francisco and Ingvaldsen, Randi B and Sperfeld, Erik and van Dijken, Gert L and Stige, Leif C and Olsen, Are and Ottersen, Geir}, title = {{Productivity in the Barents Sea - Response to Recent Climate Variability}}, journal = {PLoS ONE}, year = {2014}, volume = {9}, number = {5}, pages = {e95273}, month = may } @article{WOLYNES:1995wa, author = {WOLYNES, PG and ONUCHIC, JN and Thirumalai, D}, title = {{Models of Protein-Folding - Reply}}, journal = {Science}, year = {1995}, volume = {268}, number = {5213}, pages = {960--961} } @article{Ricker:1954eo, author = {Ricker, W E}, title = {{Stock and Recruitment}}, journal = {J. Fish. Res. Bd. Can.}, year = {1954}, volume = {11}, number = {5}, pages = {559--623}, month = may } @article{Jungwirth:2015to, author = {Jungwirth, P}, title = {{Biological Water or Rather Water in Biology?}}, journal = {J. Phys. Chem. Lett.}, year = {2015} } @article{Coffee:2005ti, author = {Coffee, Leona}, title = {{Free Executive Summary}}, year = {2005}, pages = {1--217}, month = mar } @phdthesis{Nagel:vf, author = {Nagel, Kevin}, title = {{Automatic functional annotationof predicted active sites: combining PDB and literature miningKevin Nagel}}, school = {University of Cambridge} } @article{Kuhn:2009tj, author = {Kuhn, Thomas}, title = {{The structure of scientific revolution - scan}}, year = {2009}, pages = {1--12}, month = sep } @article{Parker:2007dm, author = {Parker, H Stewart}, title = {{Reply to 'Poor trial design leaves gene therapy death a mystery'}}, journal = {Nature Medicine}, year = {2007}, volume = {13}, number = {11}, pages = {1276}, month = nov } @article{Park:2013ek, author = {Park, Jun-Koo and Jernigan, Robert and Wu, Zhijun}, title = {{Coarse Grained Normal Mode Analysis vs. Refined Gaussian Network Model for Protein Residue-Level Structural Fluctuations}}, journal = {Bull Math Biol}, year = {2013}, month = jan } @article{Zuur:2016if, author = {Zuur, Alain F and Ieno, Elena N}, title = {{A protocol for conducting and presenting results of regression-type analyses}}, journal = {Methods Ecol Evol}, year = {2016}, volume = {7}, number = {6}, pages = {636--645}, month = jun } @article{CHOTHIA:1986tm, author = {Chothia, Cyrus and Lesk, Arthur M.}, title = {{The relation between the divergence of sequence and structure in proteins.}}, journal = {Embo J}, year = {1986}, volume = {5}, number = {4}, pages = {823--826} } @article{Wust:2015bj, author = {W{\"u}st, Thomas and Reith, Daniel and Virnau, Peter}, title = {{Sequence Determines Degree of Knottedness in a Coarse-Grained Protein Model}}, journal = {Phys. Rev. Lett.}, year = {2015}, volume = {114}, number = {2}, pages = {028102}, month = jan } @article{Bakan:2009gt, author = {Bakan, Ahmet and Bahar, Ivet}, title = {{The intrinsic dynamics of enzymes plays a dominant role in determining the structural changes induced upon inhibitor binding.}}, journal = {Proc. Natl. Acad. Sci. U. S. A.}, year = {2009}, volume = {106}, number = {34}, pages = {14349--14354}, month = aug } @article{Lumb:2012jm, author = {Lumb, Craig N and Sansom, Mark S P}, title = {{Finding a Needle in a Haystack: The Role of Electrostatics in Target Lipid Recognition by PH Domains}}, journal = {PLoS Comput. Biol.}, year = {2012}, volume = {8}, number = {7}, pages = {e1002617}, month = jul } @article{Hall:1999hf, author = {Hall, David R and Leonard, Gordon A and Reed, Christopher D and Watt, C Ian and Berry, Alan and Hunter, William N}, title = {{The crystal structure of Escherichia coli class II fructose-1,6-bisphosphate aldolase in complex with phosphoglycolohydroxamate reveals details of mechanism and specificity}}, journal = {J. Mol. Biol.}, year = {1999}, volume = {287}, number = {2}, pages = {383--394}, month = mar } @article{Anonymous:pkQnXwUQ, title = {{VMD User's Guide}}, year = {2011}, pages = {1--199}, month = mar } @article{Teichert:2007ew, author = {Teichert, Florian and Bastolla, Ugo and Porto, Markus}, title = {{SABERTOOTH: protein structural alignment based on a vectorial structure representation}}, journal = {BMC Bioinformatics}, year = {2007}, volume = {8}, pages = {425} } @article{GRONEf:1990vs, author = {GRONEf, ROBERT and MERRIS, RUSSELL and SUNDER, V S}, title = {{THE LAPLACIAN SPECTRUM OF A GRAPH}}, journal = {Society for Industrial and Applied Mathematics}, year = {1990}, pages = {21} } @article{Bittova:1999kx, author = {Bittova, L and Sumandea, M and Cho, W}, title = {{A Structure-Function Study of the C2 Domain of Cytosolic Phospholipase A2: IDENTIFICATION OF ESSENTIAL CALCIUM LIGANDS AND HYDROPHOBIC MEMBRANE BINDING RESIDUES}}, journal = {J. Biol. Chem.}, year = {1999}, volume = {274}, number = {14}, pages = {9665--9672}, month = apr } @article{Mann:1947tc, author = {Mann, H B and Whitney, D R}, title = {{On a test of whether one of two random variables is stochastically larger than the other}}, journal = {The Annals of Mathematical Statistics}, year = {1947}, volume = {18}, number = {1}, pages = {50--60}, month = mar } @article{Reuveni:2010fx, author = {Reuveni, Shlomi and Granek, Rony and Klafter, Joseph J}, title = {{Anomalies in the vibrational dynamics of proteins are a consequence of fractal-like structure.}}, journal = {Proc Natl Acad Sci U S A}, year = {2010}, volume = {107}, number = {31}, pages = {13696--13700}, month = aug } @article{Kummerfeld:2009vv, author = {Kummerfeld, S and Teichmann, S}, title = {{Protein domain organisation: adding order}}, journal = {BMC Bioinformatics}, year = {2009}, volume = {10}, number = {1}, pages = {39} } @article{Hinsen:dt, author = {Hinsen, Konrad}, title = {{Software Development for Reproducible Research}}, journal = {Computing in Science {\&} Engineering}, volume = {15}, number = {4}, pages = {60--63} } @article{Anonymous:8XTHzcuh, title = {{545d2eb00cf295b5615e6925}}, year = {2003}, pages = {1--2}, month = dec } @article{Bhardwaj:2010cu, author = {Bhardwaj, Nitin and Gerstein, Mark and Lu, Hui}, title = {{Genome-wide sequence-based prediction of peripheral proteins using a novel semi-supervised learning technique}}, journal = {BMC Bioinformatics}, year = {2010}, volume = {11}, number = {Suppl 1}, pages = {S6} } @article{Doney:2013bn, author = {Doney, S C and Sailley, S F}, title = {{When an ecological regime shift is really just stochastic noise}}, journal = {Proc. Natl. Acad. Sci. U. S. A.}, year = {2013}, volume = {110}, number = {7}, pages = {2438--2439}, month = feb } @article{Furnham:2014vn, author = {Furnham, Nicholas and Holliday, Gemma L and de Beer, Tjaart A P and Jacobsen, Julius O B and Pearson, William R and Thornton, Janet M}, title = {{The Catalytic Site Atlas 2.0: cataloging catalytic sites and residues identified in enzymes}}, journal = {Nucleic acids {\ldots}}, year = {2014} } @article{LYALL:2005wa, author = {LYALL, NEIL}, title = {{THE CAUCHY-SCHWARZ INEQUALITY AND SOME SIMPLE CONSEQUENCES}}, year = {2005}, pages = {1--4}, month = jun } @article{McCammon:1999kw, author = {McCammon, J A}, title = {{Protein dynamics}}, journal = {Rep. Prog. Phys.}, year = {1984}, volume = {47}, number = {1}, pages = {1--46} } @article{HOLM:2008ci, author = {HOLM, L and Kaariainen, S and Rosenstrom, P and Schenkel, A}, title = {{Searching protein structure databases with DaliLite v.3}}, journal = {Bioinformatics}, year = {2008}, volume = {24}, number = {23}, pages = {2780}, month = dec } @article{Hinsen:2007up, author = {Hinsen, K}, title = {{Parallel scripting with Python}}, journal = {Computing in Science {\&} Engineering}, year = {2007}, pages = {82--89} } @article{Blaber:1993us, author = {Blaber, Michael and Zhang, Xue-Jun and Matthews, Brian W}, title = {{Structural basis of amino acid alpha helix propensity}}, journal = {Science}, year = {1993}, volume = {260}, number = {5114}, pages = {1637--1640} } @article{Tweten:2005dq, author = {Tweten, R K}, title = {{Cholesterol-Dependent Cytolysins, a Family of Versatile Pore-Forming Toxins}}, journal = {Infection and Immunity}, year = {2005}, volume = {73}, number = {10}, pages = {6199--6209}, month = sep } @webpage{DESAP:2017tt, author = {{DESAP}}, title = {{The European
Self Assessment Checklist for Survey Managers }}, year = {2017}, month = nov, url = {message:%3C985D25C3-2A81-4737-908B-137B7AF2CF2E@imr.no%3E} } @article{Haliloglu:2010vc, author = {Haliloglu, T and Gul, A and Erman, B}, title = {{Predicting Important Residues and Interaction Pathways in Proteins Using Gaussian Network Model: Binding and Stability of HLA Proteins}}, journal = {PLoS Comput. Biol.}, year = {2010} } @article{Kneller:2009cr, author = {Kneller, Gerald R and Hinsen, Konrad}, title = {{Quantitative model for the heterogeneity of atomic position fluctuations in proteins: A simulation study}}, journal = {J. Chem. Phys.}, year = {2009}, volume = {131}, number = {4}, pages = {045104--045104--6} } @article{Weinert:2014bj, author = {Weinert, Franz M and Brewster, Robert C and Rydenfelt, Mattias and Phillips, Rob and Kegel, Willem K}, title = {{Scaling of Gene Expression with Transcription-Factor Fugacity}}, journal = {Phys. Rev. Lett.}, year = {2014}, volume = {113}, number = {25}, pages = {258101}, month = dec } @article{Thorpe:2007hx, author = {Thorpe, M F}, title = {{Comment on elastic network models and proteins.}}, journal = {Phys. Biol.}, year = {2007}, volume = {4}, number = {1}, pages = {60--63}, month = mar } @article{HOPKINS:1991gka, author = {HOPKINS, C C E and NILSSEN, E M}, title = {{The rise and fall of the Barents Sea capelin (Mallotus villosus): a multivariate scenario}}, journal = {Polar Research}, year = {1991}, volume = {10}, number = {2}, pages = {535--546}, month = dec } @article{Langen:1998fw, author = {Langen, R and Isas, J M and Luecke, H and Haigler, H T and Hubbell, W L}, title = {{Membrane-mediated Assembly of Annexins Studied by Site-directed Spin Labeling}}, journal = {J. Biol. Chem.}, year = {1998}, volume = {273}, number = {35}, pages = {22453--22457}, month = aug } @article{Eichinger:1977fh, author = {Eichinger, B E}, title = {{An Approach to Distribution Functions for Gaussian Molecules}}, journal = {Macromolecules}, year = {1977}, volume = {10}, number = {3}, pages = {671--675}, month = may } @article{Lin:2014cn, author = {Lin, M M and Shorokhov, D and Zewail, A H}, title = {{Dominance of misfolded intermediates in the dynamics of ~-helix folding}}, journal = {Proc. Natl. Acad. Sci. U. S. A.}, year = {2014}, volume = {111}, number = {40}, pages = {14424--14429}, month = oct } @article{Giske:2011cu, author = {Giske, Jarl and Skjoldal, Hein Rune and Aksnes, Dag L}, title = {{A conceptual model of distribution of capelin in the Barents Sea}}, journal = {Sarsia}, year = {2011}, volume = {77}, number = {2}, pages = {147--156}, month = dec } @webpage{Anonymous:5o4cgER5, title = {{PLOS Computational Biology: Wikipedia Usage Estimates Prevalence of Influenza-Like Illness in the United States in Near Real-Time}}, url = {http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003581} } @article{Hayashi:2015wq, author = {Hayashi, R and Sasaki, K and Nakamura, S and Kudo, S and Inoue, Y}, title = {{Giant Acceleration of Diffusion Observed in a Single-Molecule Experiment on F 1{\textminus} ATPase}}, journal = {Phys. Rev. Lett.}, year = {2015} } @article{WolfWatz:2004gv, author = {Wolf-Watz, Magnus and Thai, Vu and Henzler-Wildman, Katherine and Hadjipavlou, Georgia and Eisenmesser, Elan Z and Kern, Dorothee}, title = {{Linkage between dynamics and catalysis in a thermophilic-mesophilic enzyme pair}}, journal = {Nature Structural {\&} Molecular Biology}, year = {2004}, volume = {11}, number = {10}, pages = {945--949}, month = aug } @article{Schaeffer:2011fe, author = {Schaeffer, R D and Jonsson, A L and Simms, A M and Daggett, V}, title = {{Generation of a consensus protein domain dictionary}}, journal = {Bioinformatics}, year = {2011}, volume = {27}, number = {1}, pages = {46--54} } @article{Liu:2014eg, author = {Liu, Yizhou and Kahn, Richard A and Prestegard, James H}, title = {{Interaction of Fapp1 with Arf1 and PI4P at a Membrane Surface: An Example of Coincidence Detection}}, journal = {Structure}, year = {2014}, volume = {22}, number = {3}, pages = {421--430}, month = mar } @article{Rizzuti:2008ij, author = {Rizzuti, Bruno and Sportelli, Luigi and Guzzi, Rita}, title = {{Molecular dynamics of amicyanin reveals a conserved dynamical core for blue copper proteins}}, journal = {Proteins: Struct., Funct., Bioinf.}, year = {2008}, volume = {74}, number = {4}, pages = {961--971} } @article{Stork:2011vd, author = {Stork, David G and Lam, Chuck P}, title = {{Open Mind Animals: Insuring the quality of data openly contributed over the World Wide Web}}, year = {2011}, pages = {1--6}, month = apr } @article{VanGorp:2011cm, author = {Van Gorp, Pieter and Mazanek, Steffen}, title = {{SHARE: a web portal for creating and sharing executable research papers}}, journal = {Procedia Computer Science}, year = {2011}, volume = {4}, pages = {589--597}, month = jan } @article{Freddolino:2010hh, author = {Freddolino, Peter L and Harrison, Christopher B and Liu, Yanxin and Schulten, Klaus}, title = {{Challenges in protein folding simulations: Timescale, representation, and analysis.}}, journal = {Nat Phys}, year = {2010}, volume = {6}, number = {10}, pages = {751--758}, month = sep } @article{FerbusZanda:2010tw, author = {Ferbus-Zanda, Marie and Grigorief, Serge}, title = {{Kolmogorov Complexity in perspective - Part I: Information Theory and Randomness}}, year = {2010}, pages = {1--40}, month = oct } @article{Anonymous:-DHHWTqF, title = {{assignment}}, year = {2005}, pages = {6} } @article{Baldwin:2007ty, author = {Baldwin, Robert L}, title = {{Energetics of protein folding}}, journal = {J. Mol. Biol.}, year = {2007}, volume = {371}, number = {2}, pages = {283--301} } @article{Lu:2014cl, author = {Lu, Xiaocun and Li, Xiaopeng and Guo, Kai and Xie, Ting-Zheng and Moorefield, Charles N and Wesdemiotis, Chrys and Newkome, George R}, title = {{Probing a Hidden World of Molecular Self-Assembly: Concentration-Dependent, Three-Dimensional Supramolecular Interconversions}}, journal = {JACS}, year = {2014}, volume = {136}, number = {52}, pages = {18149--18155}, month = dec } @article{Freiburger:2011kh, author = {Freiburger, Lee A and Baettig, Oliver M and Sprules, Tara and Berghuis, Albert M and Auclair, Karine and Mittermaier, Anthony K}, title = {{Competing allosteric mechanisms modulate substrate binding in a dimeric enzyme.}}, journal = {Nature Structural {\&} Molecular Biology}, year = {2011}, volume = {18}, number = {3}, pages = {288--294}, month = jan } @article{Lindahl:2001bm, author = {Lindahl, Erik and Hess, Berk and van der Spoel, David}, title = {{GROMACS 3.0: a package for molecular simulation and trajectory analysis}}, journal = {J Mol Model}, year = {2001}, volume = {7}, number = {8}, pages = {306--317} } @article{Pisliakov:2009ko, author = {Pisliakov, Andrei V and Cao, Jie and Kamerlin, Shina C L and Warshel, Arieh}, title = {{Enzyme millisecond conformational dynamics do not catalyze the chemical step}}, journal = {Proc. Natl. Acad. Sci. U. S. A.}, year = {2009}, volume = {106}, number = {41}, pages = {17359--17364} } @article{Leonetti:2015dz, author = {Leonetti, Giulia and Otto, Sijbren}, title = {{Solvent Composition Dictates Emergence in Dynamic Molecular Networks Containing Competing Replicators}}, journal = {JACS}, year = {2015}, volume = {137}, number = {5}, pages = {2067--2072}, month = feb } @article{Qin:2013gp, author = {Qin, Zhao and Fabre, Andrea and Buehler, Markus J}, title = {{Structure and mechanism of maximum stability of isolated alpha-helical protein domains at a critical length scale}}, journal = {Eur. Phys. J. E}, year = {2013}, volume = {36}, number = {5}, pages = {53--12}, month = may } @article{Pochapsky:2014kt, author = {Pochapsky, T C}, title = {{Examining how enzymes self-organize in a membrane}}, journal = {Proc. Natl. Acad. Sci. U. S. A.}, year = {2014}, volume = {111}, number = {10}, pages = {3659--3660}, month = mar } @article{Renetseder:vf, author = {Renetseder, R and Brunie, S and Dijkstra, B W and Drenth, J and Sigler, P B}, title = {{A comparison of the crystal structures of phospholipase A2 from bovine pancreas and Crotalus atrox venom.}}, journal = {jbc.org} } @article{Richardson:1990wd, author = {Richardson, BE}, title = {{Good vibrations (musical acoustics)}}, journal = {Physics Education}, year = {1990}, volume = {25}, pages = {35--40} } @article{Heal:2012fn, author = {Heal, J W and Jimenez-Roldan, J E and Wells, S A and Freedman, R B and Romer, R A}, title = {{Inhibition of HIV-1 protease: the rigidity perspective}}, journal = {Bioinformatics}, year = {2012}, volume = {28}, number = {3}, pages = {350--357}, month = jan } @article{Subbey:vd, author = {Subbey, Sam and Devine, Jennifer A and Schaarschmidt, Ute and Nash, Richard D M}, title = {{Modelling and forecasting stock{\textendash}recruitment: current and future perspectives}}, journal = {icesjms.oxfordjournals.org} } @article{Branduardi:2007ur, author = {Branduardi, D and Gervasio, F L and Parrinello, M}, title = {{Scitation: From A to B in free energy space}}, journal = {The Journal of chemical {\ldots}}, year = {2007} } @article{Huster:2014cp, author = {Huster, Daniel and Madhu, Perunthiruthy K}, title = {{Simplifying Solid-State NMR Spectra for Biophysical Studies on Membrane Proteins: Selective Targeting of Sites and Interactions}}, journal = {Biophys. J.}, year = {2014}, volume = {106}, number = {10}, pages = {2083--2084}, month = may } @article{Gelly:2011bi, author = {Gelly, J C and Joseph, A P and Srinivasan, N and de Brevern, A G}, title = {{iPBA: a tool for protein structure comparison using sequence alignment strategies}}, journal = {Nucleic Acids Res.}, year = {2011}, volume = {39}, number = {Web Server}, pages = {W18--W23}, month = jun } @article{Khan:2012bo, author = {Khan, S H and Awasthi, S and Guo, C and Goswami, D and Ling, J and Griffin, P R and Simons, S S and Kumar, R}, title = {{Binding of the N-terminal Region of Coactivator TIF2 to the Intrinsically Disordered AF1 Domain of the Glucocorticoid Receptor Is Accompanied by Conformational Reorganizations}}, journal = {J. Biol. Chem.}, year = {2012}, volume = {287}, number = {53}, pages = {44546--44560}, month = dec } @article{Calandrini:2010hj, author = {Calandrini, Vania and Abergel, Daniel and Kneller, Gerald R}, title = {{Fractional protein dynamics seen by nuclear magnetic resonance spectroscopy: Relating molecular dynamics simulation and experiment}}, journal = {J. Chem. Phys.}, year = {2010}, volume = {133}, number = {14}, pages = {145101} } @article{Mjanger:2016wh, author = {Mjanger, Hildegunn}, title = {{H{\AA}NDBOK FOR PR{\O}VETAKING AV FISK OG KREPSDYR}}, year = {2016}, pages = {1--193}, month = oct } @article{Yeung:2008tf, author = {Yeung, Tony and Gilbert, Gary E and Shi, Jialan and Silvius, John and Kapus, Andras and Grinstein, Sergio}, title = {{Membrane Phosphatidylserine Regulates Surface Charge and Protein Localization}}, journal = {Science, New Series}, year = {2008}, volume = {319}, number = {5860}, pages = {210--213}, month = jan } @article{Rappe:1992tb, author = {Rappe, A and Casewit, C and Colwell, K}, title = {{UFF, a full periodic table force field for molecular mechanics and molecular dynamics \ldots}}, journal = {JACS}, year = {1992} } @article{Bhabha:2011en, author = {Bhabha, G and Lee, J and Ekiert, D C and Gam, J and Wilson, I A and Dyson, H J and Benkovic, S J and Wright, P E}, title = {{A Dynamic Knockout Reveals That Conformational Fluctuations Influence the Chemical Step of Enzyme Catalysis}}, journal = {Science}, year = {2011}, volume = {332}, number = {6026}, pages = {234--238}, month = apr } @article{Keskin:2008up, author = {Keskin, O and Gursoy, A and Ma, B and Nussinov, R}, title = {{Principles of Protein{\textminus} Protein Interactions: What are the Preferred Ways For Proteins To Interact?}}, journal = {Chem. Rev}, year = {2008}, volume = {108}, number = {4}, pages = {1225--1244} } @article{Stapleton:1980cm, author = {Stapleton, H and Allen, J and Flynn, C and Stinson, D and Kurtz, S}, title = {{Fractal Form of Proteins}}, journal = {Phys. Rev. Lett.}, year = {1980}, volume = {45}, number = {17}, pages = {1456--1459}, month = oct } @article{Motlagh:2012bj, author = {Motlagh, Hesam N and Hilser, Vincent J}, title = {{Agonism/antagonism switching in allosteric ensembles.}}, journal = {Proc. Natl. Acad. Sci. U. S. A.}, year = {2012}, volume = {109}, number = {11}, pages = {4134--4139}, month = mar } @article{Mecozzi:1996td, author = {Mecozzi, S and West, A P and Dougherty, D A}, title = {{Cation-pi interactions in aromatics of biological and medicinal interest: electrostatic potential surfaces as a useful qualitative guide.}}, journal = {Proc Natl Acad Sci U S A}, year = {1996}, volume = {93}, number = {20}, pages = {10566--10571}, month = oct } @article{Lyon:2014gw, author = {Lyon, Angeline M and Begley, Jessica A and Manett, Taylor D and Tesmer, John J G}, title = {{Molecular Mechanisms of Phospholipase C $\beta$3 Autoinhibition}}, journal = {Structure}, year = {2014}, volume = {22}, number = {12}, pages = {1844--1854}, month = dec } @article{Mouchlis:tr, author = {Mouchlis, Varnavas D and Bucher, Denis and McCammon, J Andrew and Dennis, Edward A}, title = {{Membranes serve as allosteric activators of phospholipase A2, enabling it to extract, bind, and hydrolyze phospholipid substrates}}, journal = {pnas.org} } @article{Lee:2009ir, author = {Lee, Seungjoo and Antony, Lizamma and Hartmann, Rune and Knaus, Karen J and Surewicz, Krystyna and Surewicz, Witold K and Yee, Vivien C}, title = {{Conformational diversity in prion protein variants influences intermolecular beta-sheet formation}}, journal = {Embo J}, year = {2010}, volume = {29}, number = {1}, pages = {251--262} } @article{Lobo:2008vl, author = {Lobo, JM and Jim{\'e}nez-Valverde, A}, title = {{AUC: a misleading measure of the performance of predictive distribution models}}, journal = {Global Ecology and Biogeography}, year = {2008} } @article{MORITSUGU:2007bq, author = {Moritsugu, Kei and Smith, Jeremy C}, title = {{Coarse-Grained Biomolecular Simulation with REACH: Realistic Extension Algorithm via Covariance Hessian}}, journal = {Biophys. J.}, year = {2007}, volume = {93}, number = {10}, pages = {3460--3469}, month = nov } @article{Kelkar:2006fy, author = {Kelkar, Devaki A and Chattopadhyay, Amitabha}, title = {{Membrane interfacial localization of aromatic amino acids and membrane protein function}}, journal = {J Biosci}, year = {2006}, volume = {31}, number = {3}, pages = {297--302}, month = sep } @article{Dougherty:2007uo, author = {Dougherty, Dennis A}, title = {{Cation-pi interactions involving aromatic amino acids.}}, journal = {J. Nutr.}, year = {2007}, volume = {137}, number = {6 Suppl 1}, pages = {1504S--1508S-- discussion 1516S--1517S}, month = jun } @article{Poupon:2004bk, author = {Poupon, Anne}, title = {{Voronoi and Voronoi-related tessellations in studies of protein structure and interaction.}}, journal = {Current Opinion in Structural Biology}, year = {2004}, volume = {14}, number = {2}, pages = {233--241}, month = apr } @article{Deber:2002ug, author = {Deber, CM and Therien, AG}, title = {{Putting the $\beta$-breaks on membrane protein misfolding}}, journal = {Nature Structural {\&} Molecular Biology}, year = {2002}, volume = {9}, number = {5}, pages = {318--319} } @article{Whited:2015kp, author = {Whited, A M and Johs, A}, title = {{The interactions of peripheral membrane proteins with biological membranes}}, journal = {Chemistry and Physics of Lipids}, year = {2015}, volume = {192}, pages = {51--59}, month = nov } @article{Motiejunas:2008kr, author = {Motiejunas, Domantas and Gabdoulline, Razif and Wang, Ting and Feldman-Salit, Anna and Johann, Tim and Winn, Peter J and Wade, Rebecca C}, title = {{Protein-protein docking by simulating the process of association subject to biochemical constraints}}, journal = {Proteins: Struct., Funct., Bioinf.}, year = {2008}, volume = {71}, number = {4}, pages = {1955--1969} } @article{Zhang:2006kt, author = {Zhang, Jinfeng and Liu, Jun S}, title = {{On Side-Chain Conformational Entropy of Proteins}}, journal = {PLoS Comput. Biol.}, year = {2006}, volume = {2}, number = {12}, pages = {e168}, month = dec } @article{Anonymous:SnxG2oom, title = {{hungarian}}, year = {2004}, pages = {8}, month = oct } @article{Hinsen:2005jr, author = {Hinsen, K and Reuter, N and Navaza, J and Stokes, DL and Lacapere, JJ}, title = {{Normal mode-based fitting of atomic structure into electron density maps: Application to sarcoplasmic reticulum Ca-ATPase}}, journal = {Biophys. J.}, year = {2005}, volume = {88}, number = {2}, pages = {818--827} } @article{Subbey:2017dk, author = {Subbey, Sam}, title = {{Regularization of a Parameter Estimation Problem using Monotonicity and Convexity Constraints}}, journal = {ESAIM: ProcS}, year = {2017}, volume = {57}, pages = {86--96}, month = oct } @article{VOJTECHOVSKY:1999dp, author = {VOJTECHOVSKY, J}, title = {{Crystal Structures of Myoglobin-Ligand Complexes at Near-Atomic Resolution}}, journal = {Biophys. J.}, year = {1999}, volume = {77}, number = {4}, pages = {2153--2174}, month = oct } @article{Aloy:2006fd, author = {Aloy, Patrick and Russell, Robert B}, title = {{Structural systems biology: modelling protein interactions}}, journal = {Nat Rev Mol Cell Biol}, year = {2006}, volume = {7}, number = {3}, pages = {188--197}, month = mar } @article{Christiansen:2008hv, author = {Christiansen, Jorgen S and Praebel, Kim and Siikavuopio, Sten I and Carscadden, James E}, title = {{Facultative semelparity in capelin Mallotus villosus (Osmeridae) - an experimental test of a life history phenomenon in a sub-arctic fish}}, journal = {Journal of Experimental Marine Biology and Ecology}, year = {2008}, volume = {360}, number = {1}, pages = {47--55} } @article{Pauli:2012ip, author = {Pauli, A and Valen, E and Lin, M F and Garber, M and Vastenhouw, N L and Levin, J Z and Fan, L and Sandelin, A and Rinn, J L and Regev, A and Schier, A F}, title = {{Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis}}, journal = {Genome Res}, year = {2012}, volume = {22}, number = {3}, pages = {577--591}, month = mar } @article{Amadel:2006tq, author = {Amadel, Andrea and Linssen, Antonius BM and Berendsen, Herman JC}, title = {{Essential Dynamics of Proteins}}, year = {2006}, pages = {1--14}, month = nov } @article{Vijayabaskar:2011tq, author = {Vijayabaskar, M S and Niranjan, V and Vishveshwara, S}, title = {{GraProStr{\textendash}Graphs of Protein Structures: A Tool for Constructing the Graphs and Generating Graph Parameters for Protein Structures}}, journal = {Open Bioinformatics Journal}, year = {2011}, volume = {5}, pages = {53--58} } @article{Uversky:2005cu, author = {Uversky, Vladimir N and Oldfield, Christopher J and Dunker, A Keith}, title = {{Showing your ID: intrinsic disorder as an ID for recognition, regulation and cell signaling}}, journal = {J. Mol. Recognit.}, year = {2005}, volume = {18}, number = {5}, pages = {343--384} } @article{England:2003kz, author = {England, JL and Shakhnovich, EI}, title = {{Structural determinant of protein designability}}, journal = {Phys. Rev. Lett.}, year = {2003}, volume = {90}, number = {21}, pages = {218101} } @article{MacCallum:2011ci, author = {MacCallum, Justin L and Tieleman, D Peter}, title = {{Hydrophobicity scales:a thermodynamic looking glass intolipid}}, journal = {Trends in Biochemical Sciences}, year = {2011}, volume = {36}, number = {12}, pages = {653--662}, month = dec } @article{White:1998wb, author = {White, S H and Wimley, W C}, title = {{Hydrophobic interactions of peptides with membrane interfaces.}}, journal = {Biochim. Biophys. Acta}, year = {1998}, volume = {1376}, number = {3}, pages = {339--352}, month = nov } @article{Keskin:2000ub, author = {Keskin, O and Jernigan, RL and Bahar, I}, title = {{Proteins with similar architecture exhibit similar large-scale dynamic behavior}}, journal = {Biophys. J.}, year = {2000}, volume = {78}, number = {4}, pages = {2093--2106} } @article{CHOU:1983um, author = {CHOU, KC}, title = {{Identification of Low-Frequency Modes in Protein Molecules}}, journal = {Biochem J}, year = {1983}, volume = {215}, number = {3}, pages = {465--469} } @article{Unverdorben:wh, author = {Unverdorben, Pia and Beck, Florian and {\'{S}}led{\'{z}}, Pawe{\l} and Schweitzer, Andreas and Pfeifer, G{\"u}nter and Plitzko, J{\"u}rgen M and Baumeister, Wolfgang and F{\"o}rster, Friedrich}, title = {{Deep classification of a large cryo-EM dataset defines the conformational landscape of the 26S proteasome}}, journal = {pnas.org} } @article{Jackson:2000ds, author = {Jackson, Graham S and Clarke, Anthony R}, title = {{Mammalian prion proteins}}, journal = {Current Opinion in Structural Biology}, year = {2000}, volume = {10}, number = {1}, pages = {69--74}, month = feb } @article{Lu:2011dl, author = {Lu, Mingyang and Ma, Jianpeng}, title = {{Normal mode analysis with molecular geometry restraints: Bridging molecular mechanics and elastic models}}, journal = {Arch Biochem Biophys}, year = {2011}, volume = {508}, number = {1}, pages = {64--71} } @article{Gregoire:1998im, author = {Gregoire, T G}, title = {{Design-based and model-based inference in survey sampling: appreciating the difference}}, journal = {Canadian Journal of Forest Research}, year = {1998}, volume = {28}, number = {10}, pages = {1429--1447} } @article{Hinsen:2009ub, author = {Hinsen, K}, title = {{Physical arguments for distance-weighted interactions in elastic network models for proteins}}, journal = {Proc. Natl. Acad. Sci. U. S. A.}, year = {2009} } @article{Mitternacht:2011bo, author = {Mitternacht, Simon and Berezovsky, Igor N.}, title = {{Coherent conformational degrees of freedom as a structural basis for allosteric communication.}}, journal = {PLoS Comput. Biol.}, year = {2011}, volume = {7}, number = {12}, pages = {e1002301}, month = dec } @article{Cacciatore:wh, author = {Cacciatore, Stefano and Luchinat, Claudio and Tenori, Leonardo}, title = {{Knowledge discovery by accuracy maximization}}, journal = {pnas.org} } @article{Bakan:2011jc, author = {Bakan, Ahmet and Meireles, Lidio M and Bahar, Ivet}, title = {{ProDy: protein dynamics inferred from theory and experiments.}}, journal = {Bioinformatics}, year = {2011}, volume = {27}, number = {11}, pages = {1575--1577}, month = jun } @article{Reeves:2006jt, author = {Reeves, Gabrielle A and Dallman, Timothy J and Redfern, Oliver C and Akpor, Adrian and Orengo, Christine A}, title = {{Structural diversity of domain superfamilies in the CATH database}}, journal = {J. Mol. Biol.}, year = {2006}, volume = {360}, number = {3}, pages = {725--741} } @article{Jin:2014dc, author = {Jin, Qiyu and Sorzano, Carlos Oscar S and de la Rosa-Trev{\'\i}n, Jos{\'e} Miguel and Bilbao-Castro, Jos{\'e} Rom{\'a}n and N{\'u}{\~n}ez-Ram{\'\i}rez, Rafael and Llorca, Oscar and Tama, Florence and Joni{\'c}, Slavica}, title = {{Iterative Elastic 3D-to-2D Alignment Method Using Normal Modes for Studying Structural Dynamics of Large Macromolecular Complexes}}, journal = {Structure}, year = {2014}, volume = {22}, number = {3}, pages = {496--506}, month = mar } @article{Zeldovich:2007ga, author = {Zeldovich, Konstantin B and Chen, Peiqiu and Shakhnovich, Boris E and Shakhnovich, Eugene I}, title = {{A First-Principles Model of Early Evolution: Emergence of Gene Families, Species, and Preferred Protein Folds}}, journal = {PLoS Comput. Biol.}, year = {2007}, volume = {3}, number = {7}, pages = {e139} } @article{Harper:wSdCyJQZ, author = {Harper, Robert}, title = {{Practical Foundations for Programming Languages}} } @article{Ings:2008vp, author = {Ings, S}, title = {{Darwin 200: An eye for the eye.}}, journal = {Nature}, year = {2008} } @article{Nishi:2014ho, author = {Nishi, Hafumi and Shaytan, Alexey and Panchenko, Anna R}, title = {{Physicochemical mechanisms of protein regulation by phosphorylation}}, journal = {Front. Psychiatry}, year = {2014}, volume = {5} } @article{Citron:uk, author = {Citron, Daniel T and Ginsparg, Paul}, title = {{Patterns of text reuse in a scientific corpus}}, journal = {pnas.org} } @article{Moritsugu:2009jq, author = {Moritsugu, Kei and Kurkal-Siebert, Vandana and Smith, Jeremy C}, title = {{REACH coarse-grained normal mode analysis of protein dimer interaction dynamics}}, journal = {Biophys. J.}, year = {2009}, volume = {97}, number = {4}, pages = {1158--1167}, month = aug } @article{Fraser:wm, author = {Fraser, James S and van den Bedem, Henry and Samelson, Avi J and Lang, P Therese and Holton, James M and Echols, Nathaniel and Alber, Tom}, title = {{Accessing protein conformational ensembles using room-temperature X-ray crystallography}}, journal = {pnas.org} } @article{Law:uy, author = {Law, Sean M and Gagnon, Jessica K and Mapp, Anna K and Brooks, Charles L}, title = {{Prepaying the entropic cost for allosteric regulation in KIX}}, journal = {pnas.org} } @article{Alexopoulos:1994ww, author = {Alexopoulos, C}, title = {{JSTOR: Management Science, Vol. 40, No. 12 (Dec., 1994), pp. 1748-1763}}, journal = {Management Science}, year = {1994} } @article{Micsonai:wc, author = {Micsonai, Andr{\'a}s and Wien, Frank and Kernya, Linda and Lee, Young-Ho and Goto, Yuji and R{\'e}fr{\'e}giers, Matthieu and Kardos, J{\'o}zsef}, title = {{Accurate secondary structure prediction and fold recognition for circular dichroism spectroscopy}}, journal = {pnas.org} } @article{Kim:2002df, author = {Kim, Moon K and Jernigan, Robert L and Chirikjian, Gregory S}, title = {{Efficient generation of feasible pathways for protein conformational transitions.}}, journal = {Biophysj}, year = {2002}, volume = {83}, number = {3}, pages = {1620--1630}, month = sep } @article{Bay:2013hp, author = {Bay, Denice C and Turner, Raymond J}, title = {{Membrane composition influences the topology bias of bacterial integral membrane proteins}}, journal = {Biochimica et Biophysica Acta (BBA) - Biomembranes}, year = {2013}, volume = {1828}, number = {2}, pages = {260--270}, month = feb } @article{Signorini:2014cc, author = {Signorini, Giorgio F and Giovannelli, Edoardo and Spill, Yannick G and Nilges, Michael and Chelli, Riccardo}, title = {{Convective Replica-Exchange in Ergodic Regimes}}, journal = {J Chem Theory Comput}, year = {2014}, volume = {10}, number = {3}, pages = {953--958}, month = mar } @article{Micheletti:2001vz, author = {Micheletti, C and Seno, F and Banavar, JR and Maritan, A}, title = {{Learning effective amino acid interactions through iterative stochastic techniques}}, journal = {Proteins: Struct., Funct., Bioinf.}, year = {2001}, volume = {42}, number = {3}, pages = {422--431} } @article{Andreeva:2006iga, author = {Andreeva, A and Murzin, A}, title = {{Evolution of protein fold in the presence of functional constraints}}, journal = {Current Opinion in Structural Biology}, year = {2006}, volume = {16}, number = {3}, pages = {399--408}, month = jun } @article{Ichiye:1991te, author = {Ichiye, T and Karplus, M}, title = {{Collective motions in proteins - a covariance analysis of atomic fluctuations in molecular-dynamics and normal mode simulations}}, journal = {Proteins: Struct., Funct., Bioinf.}, year = {1991}, volume = {11}, number = {3}, pages = {205--217} } @article{Hinsen:2014jb, author = {Hinsen, Konrad}, title = {{Computational science: shifting the focus from tools to models}}, journal = {F1000Res}, year = {2014}, month = jun } @article{Bogdanov:2013ue, author = {Bogdanov, M and Dowhan, W and Vitrac, H}, title = {{Lipids and topological rules governing membrane protein assembly}}, journal = {Biochimica et Biophysica Acta (BBA)- {\ldots}}, year = {2013} } @article{Parulek:2013cd, author = {Parulek, Julius and Turkay, Cagatay and Reuter, Nathalie and Viola, Ivan}, title = {{Visual cavity analysis in molecular simulations}}, journal = {BMC Bioinformatics}, year = {2013}, volume = {14}, number = {Suppl 19}, pages = {S4}, month = nov } @article{Campagna:2008fx, author = {Campagna, Anne and Serrano, Luis and Kiel, Christina}, title = {{Shaping dots and lines: Adding modularity into protein interaction networks using structural information}}, journal = {Febs Lett}, year = {2008}, volume = {582}, number = {8}, pages = {1231--1236} } @article{Huang:2000iv, author = {Huang, D M and Chandler, D}, title = {{Temperature and length scale dependence of hydrophobic effects and their possible implications for protein folding}}, journal = {Proc. Natl. Acad. Sci. U. S. A.}, year = {2000}, volume = {97}, number = {15}, pages = {8324--8327}, month = jul } @article{Lyman:2008fi, author = {Lyman, Edward and Pfaendtner, Jim and Voth, Gregory A}, title = {{Systematic multiscale parameterization of heterogeneous elastic network models of proteins.}}, journal = {Biophys. J.}, year = {2008}, volume = {95}, number = {9}, pages = {4183--4192}, month = nov } @article{MacKerell:2001gb, author = {MacKerell, Alexander D and Banavali, Nilesh and Foloppe, Nicolas}, title = {{Development and current status of the CHARMM force field for nucleic acids}}, journal = {Biopolymers}, year = {2001}, volume = {56}, number = {4}, pages = {257--265} } @article{Anonymous:vr2dt-Sw, title = {{ess}}, year = {2007}, pages = {3} } @article{DSSP:eipI_aYB, author = {Hekkelman, Marteen}, title = {{DSSP}} } @article{Dunbrack:2006wb, author = {Dunbrack, RL}, title = {{Sequence comparison and protein structure prediction}}, journal = {Current Opinion in Structural Biology}, year = {2006}, volume = {16}, number = {3}, pages = {374--384} } @unpublished{Fuglebakk:BHKn2tsT, author = {Fuglebakk, Edvin and Reuter, Nathalie and Hinsen, Konrad}, title = {{Inter-residue covariance predictions from protein elastic network models}} } @article{Aliste:2005bh, author = {Aliste, MarcelaP and Tieleman, D Peter}, title = {{Computer simulation of partitioning of ten pentapeptides Ace-WLXLL at the cyclohexane/water and phospholipid/water interfaces}}, journal = {BMC Biochem}, year = {2005}, volume = {6}, number = {1}, pages = {30} } @article{Hall:2002vc, author = {Hall, David R and Bond, Charles S and Leonard, Gordon A and Watt, C Ian and Berry, Alan and Hunter, William N}, title = {{Structure of Tagatose-1,6-bisphosphate Aldolase}}, journal = {Journal of Biological {\ldots}}, year = {2002} } @article{Baggerly:2009tm, author = {Baggerly, By Keith A and Coombes, Kevin R}, title = {{DERIVING CHEMOSENSITIVITY FROM CELL LINES: FORENSIC BIOINFORMATICS AND REPRODUCIBLE RESEARCH IN HIGH-THROUGHPUT BIOLOGY }}, journal = {Annals of Applied Statistics (submitted)}, year = {2009}, pages = {1--26}, month = sep } @article{MacKay:2009wc, author = {MacKay, David JC}, title = {{Information Theory Inference and Learning Algorithms}}, year = {2009}, pages = {1--640}, month = sep } @article{Galimzyanov:2015vd, author = {Galimzyanov, T R and Molotkovsky, R J and Bozdaganyan, M E}, title = {{Elastic Membrane Deformations Govern Interleaflet Coupling of Lipid-Ordered Domains}}, journal = {Phys. Rev. Lett.}, year = {2015} } @article{Schaarschmidt:2018cx, author = {Schaarschmidt, Ute and Steihaug, Trond and Subbey, Sam}, title = {{A parametrized stock-recruitment relationship derived from a slow-fast population dynamic model}}, journal = {Mathematics and Computers in Simulation}, year = {2018}, volume = {145}, pages = {171--185}, month = mar } @article{Orengo:1997fp, author = {Orengo, C A and Michie, A D and Jones, S and Jones, D T and Swindells, M B and Thornton, J M}, title = {{CATH {\textendash} a hierarchic classification of protein domain structures}}, journal = {Structure}, year = {1997}, volume = {5}, number = {8}, pages = {1093--1108}, month = aug } @article{Ferrada:2008dz, author = {Ferrada, Evandro and Wagner, Andreas}, title = {{Protein robustness promotes evolutionary innovations on large evolutionary time-scales}}, journal = {Proceedings of the Royal Society B: Biological Sciences}, year = {2008}, volume = {275}, number = {1643}, pages = {1595--1602}, month = apr } @article{Fenley:2012ev, author = {Fenley, A T and Muddana, H S and Gilson, M K}, title = {{Entropy-enthalpy transduction caused by conformational shifts can obscure the forces driving protein-ligand binding}}, journal = {Proc. Natl. Acad. Sci. U. S. A.}, year = {2012}, volume = {109}, number = {49}, pages = {20006--20011}, month = dec } @article{Pandini:2012df, author = {Pandini, Alessandro and Fornili, Arianna and Fraternali, Franca and Kleinjung, Jens}, title = {{Detection of allosteric signal transmission by information-theoretic analysis of protein dynamics.}}, journal = {FASEB J.}, year = {2012}, volume = {26}, number = {2}, pages = {868--881}, month = feb } @article{Naughton:2016kt, author = {Naughton, Fiona B and Kalli, Antreas C and Sansom, Mark S P}, title = {{Association of Peripheral Membrane Proteins with Membranes: Free Energy of Binding of GRP1 PH Domain with Phosphatidylinositol Phosphate-Containing Model Bilayers}}, journal = {J. Phys. Chem. Lett.}, year = {2016}, volume = {7}, number = {7}, pages = {1219--1224}, month = apr } @article{DWHeinz:1995wo, author = {Heinz, Dirk W and Ryan, Margret and Bullock, Timothy L and Griffith, O Hayes}, title = {{Crystal structure of the phosphatidylinositol-specific phospholipase C from Bacillus cereus in complex with myo-inositol.}}, journal = {Embo J}, year = {1995}, volume = {14}, number = {16}, pages = {3855--3863}, month = aug } @book{Fukunaga:1990wj, author = {Fukunaga, Keinosuke}, editor = {Rheinboldt, Weiner}, title = {{Introduction to Statistical Pattern Recognition}}, publisher = {Academic Press}, year = {1990}, edition = {2nd} } @article{HOLM:1993uq, author = {HOLM, L and SANDER, C}, title = {{Protein Structure Comparison by Alignment of Distance Matrices}}, journal = {J. Mol. Biol.}, year = {1993} } @article{Ochman:2000um, author = {Ochman, Howard and Lawrence, Jeffrey G and Groisman, Eduardo A}, title = {{Later al gene tr ansfer and the nature of bacterial innovation}}, journal = {Nature}, year = {2000}, pages = {1--6} } @book{Anonymous:2012ta, publisher = {Springer New York}, year = {2012}, address = {New York, NY}, month = nov } @article{WongEkkabut:2008hy, author = {Wong-Ekkabut, Jirasak and Baoukina, Svetlana and Triampo, Wannapong and Tang, I-Ming and Tieleman, D Peter and Monticelli, Luca}, title = {{Computer simulation study of fullerene translocation through lipid membranes}}, journal = {Nature Nanotech}, year = {2008}, volume = {3}, number = {6}, pages = {363--368}, month = may } @article{Smith:ohMGyjIe, author = {Smith, Lindsay I}, title = {{A tutorial on Principal Components Analysis}}, year = {2002}, pages = {27}, month = feb } @article{LoConte:2002ut, author = {Lo Conte, Loredana and Brenner, Steven E. and Hubbard, Tim J. P. and Chothia, Cyrus and Murzin, Alexey G}, title = {{SCOP database in 2002: refinements accommodate structural genomics}}, journal = {Nucleic Acids Res.}, year = {2002}, volume = {30}, number = {1}, pages = {264--267} } @article{Lopez:2009dq, author = {Lopez, Daniel and Pazos, Florencio}, title = {{Gene ontology functional annotations at the structural domain level.}}, journal = {Proteins: Struct., Funct., Bioinf.}, year = {2009}, volume = {76}, number = {3}, pages = {598--607}, month = aug } @article{Borga:2011ur, author = {Borga, Magnus}, title = {{Canonical correlation - a tutorial}}, year = {2011}, pages = {1--12}, month = nov } @article{Berendsen:1995vz, author = {Berendsen, HJC and van der Spoel, D}, title = {{ScienceDirect.com - Computer Physics Communications - GROMACS: A message-passing parallel molecular dynamics implementation}}, journal = {Computer Physics {\ldots}}, year = {1995} } @article{Reuter:2003tf, author = {Reuter, Nathalie and Hinsen, Konrad and Lacap{\`e}re, Jean-Jacques}, title = {{Transconformations of the SERCA1 Ca-ATPase: A Normal Mode Study}}, journal = {Biophys. J.}, year = {2003}, volume = {85}, number = {4}, pages = {2186--2197}, month = oct } @article{Prabhu:2005ep, author = {Prabhu, Ninad V and Sharp, Kim A}, title = {{HEAT CAPACITY IN PROTEINS}}, journal = {Annu. Rev. Phys. Chem.}, year = {2005}, volume = {56}, number = {1}, pages = {521--548}, month = may } @article{Sethna:2009ue, author = {Sethna, James P}, title = {{Entropy, Order Parameters, and Complexity}}, year = {2009}, pages = {1--371}, month = apr } @webpage{Anonymous:rxEz8eEN, title = {{Interactions of the fatty acid-binding protein ReP1-NCXSQ with lipid membranes. Influence of the membrane electric field on binding and orientation}}, url = {http://www.sciencedirect.com/science/article/pii/S0005273613004057} } @article{Shurki:2004wl, author = {Shurki, A and Warshel, A}, title = {{Why does the Ras switch ``break'' by oncogenic mutations?}}, journal = {Proteins: Struct., Funct., Bioinf.}, year = {2004}, volume = {55}, number = {1}, pages = {1--10} } @article{Haliloglu:2005hq, author = {Haliloglu, T}, title = {{How Similar Are Protein Folding and Protein Binding Nuclei? Examination of Vibrational Motions of Energy Hot Spots and Conserved Residues}}, journal = {Biophys. J.}, year = {2005}, volume = {88}, number = {3}, pages = {1552--1559}, month = mar } @article{Gilbert:2002ja, author = {Gilbert, G E and Kaufman, R J and Arena, A A and Miao, H and Pipe, S W}, title = {{Four Hydrophobic Amino Acids of the Factor VIII C2 Domain Are Constituents of Both the Membrane-binding and von Willebrand Factor-binding Motifs}}, journal = {J. Biol. Chem.}, year = {2002}, volume = {277}, number = {8}, pages = {6374--6381}, month = feb } @article{Perica:2012hp, author = {Perica, Tina and Chothia, Cyrus and Teichmann, Sarah A}, title = {{Evolution of oligomeric state through geometric coupling of protein interfaces}}, journal = {Proc Natl Acad Sci U S A}, year = {2012}, volume = {109}, number = {21}, pages = {8127--8132} } @article{Papaleo:2006ut, author = {Papaleo, E and Riccardi, L and Villa, C and Fantucci, P and De Gioia, L}, title = {{Flexibility and enzymatic cold-adaptation: A comparative molecular dynamics investigation of the elastase family}}, journal = {BBA-Proteins and Proteomics}, year = {2006}, volume = {1764}, number = {8}, pages = {1397--1406} } @article{Barber:1996iv, author = {Barber, C Bradford and Dobkin, David P and Huhdanpaa, Hannu}, title = {{The quickhull algorithm for convex hulls}}, journal = {ACM Trans. Math. Softw.}, year = {1996}, volume = {22}, number = {4}, pages = {469--483}, month = dec } @article{Du:2012et, author = {Du, Qi-Shi and Meng, Jian-Zong and Liao, Si-Ming and Huang, Ri-Bo}, title = {{Energies and physicochemical properties of cation{\textendash}$\pi$ interactions in biological structures}}, journal = {Biophys. J.}, year = {2012}, volume = {34}, pages = {38--45}, month = apr } @book{steele1974structure, author = {Steele, J H}, title = {{The structure of marine ecosystems}}, publisher = {Harvard University Press}, year = {1974} } @booklet{Cooper:uc, title = {{A guide to Fisheries Stock Assessment}}, author = {Cooper, Andrew B}, howpublished = {seagrant.unh.edu} } @article{Tokuriki:2009bz, author = {Tokuriki, Nobuhiko and Tawfik, Dan S}, title = {{Protein Dynamism and Evolvability}}, journal = {Science}, year = {2009}, volume = {324}, number = {5924}, pages = {203--207} } @article{WOLYNES:1995tj, author = {WOLYNES, PG and ONUCHIC, JN and Thirumalai, D}, title = {{Navigating the Folding Routes}}, journal = {Science}, year = {1995}, volume = {267}, number = {5204}, pages = {1619--1620} } @article{Lazaridis:2004id, author = {Lazaridis, Themis}, title = {{Implicit solvent simulations of peptide interactions with anionic lipid membranes}}, journal = {Proteins: Struct., Funct., Bioinf.}, year = {2004}, volume = {58}, number = {3}, pages = {518--527}, month = dec } @article{Toncrova:2010ida, author = {Toncrova, Hedvika and McLeish, Tom C B}, title = {{Substrate-Modulated Thermal Fluctuations Affect Long-Range Allosteric Signaling in Protein Homodimers: Exemplified in CAP}}, journal = {Biophys. J.}, year = {2010}, volume = {98}, number = {10}, pages = {2317--2326}, month = may } @article{Hanson:2010hx, author = {Hanson, Robert M}, title = {{Jmol{\textendash} a paradigm shift in crystallographic visualization}}, journal = {J Appl Crystallogr}, year = {2010}, volume = {43}, number = {5}, pages = {1250--1260}, month = sep } @article{Radzicka:1988bt, author = {Radzicka, Anna and Wolfenden, Richard}, title = {{Comparing the polarities of the amino acids: side-chain distribution coefficients between the vapor phase, cyclohexane, 1-octanol, and neutral aqueous solution}}, journal = {Biochemistry}, year = {1988}, volume = {27}, number = {5}, pages = {1664--1670}, month = mar } @article{Aflalo:tz, author = {Aflalo, Yonathan and Bronstein, Alexander and Kimmel, Ron}, title = {{On convex relaxation of graph isomorphism}}, journal = {pnas.org} } @article{Pettersson:2016hp, author = {Pettersson, Lars Gunnar Moody and Henchman, Richard Humfry and Nilsson, Anders}, title = {{Water{\textemdash}The Most Anomalous Liquid}}, journal = {Chem. Rev}, year = {2016}, volume = {116}, number = {13}, pages = {7459--7462}, month = jul } @article{Aanes:2015gsa, author = {Aanes, Sondre and V{\o}lstad, Jon Helge and Trenkel, Verena}, title = {{Efficient statistical estimators and sampling strategies for estimating the age composition of fish}}, journal = {Canadian Journal of Fisheries and Aquatic Sciences}, year = {2015}, volume = {72}, number = {6}, pages = {938--953}, month = jun } @article{Anonymous:-UG-QrMl, title = {{A geometric revier of linear algebra}}, year = {2009}, pages = {1--10}, month = feb } @article{Fraczkiewicz:1998wn, author = {Fraczkiewicz, R and Braun, W}, title = {{Exact and efficient analytical calculation of the accessible surface areas and their gradients for macromolecules}}, journal = {J. Comput. Chem.}, year = {1998} } @article{Anonymous:fJsxWeuz, author = {{euroscreen}}, title = {{euroscreen manual}}, year = {2007}, pages = {1--2}, month = dec } @article{MulgrewNesbitt:2006dy, author = {Mulgrew-Nesbitt, Anna and Diraviyam, Karthikeyan and Wang, Jiyao and Singh, Shaneen and Murray, Paul and Li, Zhaohui and Rogers, Laura and Mirkovic, Nebojsa and Murray, Diana}, title = {{The role of electrostatics in protein-membrane interactions.}}, journal = {Biochim. Biophys. Acta}, year = {2006}, volume = {1761}, number = {8}, pages = {812--826}, month = aug } @article{Clark:2015ce, author = {Clark, Alex M and Ekins, Sean}, title = {{Open Source Bayesian Models. 2. Mining a {\textquotedblleft}Big Dataset{\textquotedblright} To Create and Validate Models with ChEMBL}}, journal = {J Chem Inf Model}, year = {2015}, volume = {55}, number = {6}, pages = {1246--1260}, month = jun } @article{Benoit:2009gq, author = {Beno{\^\i}t, Hugues P and Allard, Jacques}, title = {{Can the data from at-sea observer surveys be used to make general inferences about catch composition and discards?}}, journal = {Canadian Journal of Fisheries and Aquatic Sciences}, year = {2009}, volume = {66}, number = {12}, pages = {2025--2039}, month = dec } @article{Johnson:2013cv, author = {Johnson, Valen E}, title = {{Revised standards for statistical evidence}}, journal = {Proc Natl Acad Sci U S A}, year = {2013}, volume = {110}, number = {48}, pages = {19313--19317}, month = nov } @article{Gjosaeter:1998vm, author = {Gjosaeter, H and Bogstad, B}, title = {{Effects of the presence of herring (Clupea harengus) on the stock-recruitment relationship of Barents Sea capelin (Mallotus villosus)}}, journal = {Fisheries Research}, year = {1998}, volume = {38}, number = {1}, pages = {57--71}, month = sep } @article{Baumbach:2009td, author = {Baumbach, Jan and Wittkop, Tobias and Kleindt, Christiane Katja and Tauch, Andreas}, title = {{Integrated analysis and reconstruction of microbial transcriptional gene regulatory networks using CoryneRegNet }}, year = {2009}, pages = {1--28}, month = mar, annote = {Notes } } @article{Berendsen:2000tt, author = {Berendsen, Herman JC and Hayward, Steven}, title = {{Collective protein dynamics in relation to function.}}, journal = {Current Opinion in Structural Biology}, year = {2000}, volume = {10}, number = {2}, pages = {165--169} } @article{Robertson:1981ur, author = {Robertson, J D}, title = {{Membrane structure.}}, journal = {The Journal of Cell Biology}, year = {1981} } @article{Ghosh:2015du, author = {Ghosh, Ujjayini and Xie, Li and Jia, Lihui and Liang, Shuang and Weliky, David P}, title = {{Closed and Semiclosed Interhelical Structures in Membrane vs Closed and Open Structures in Detergent for the Influenza Virus Hemagglutinin Fusion Peptide and Correlation of Hydrophobic Surface Area with Fusion Catalysis}}, journal = {JACS}, year = {2015}, volume = {137}, number = {24}, pages = {7548--7551}, month = jun } @article{Amber03, author = {Duan, Yong and Wu, Chun and Chowdhury, Shibasish and Lee, Mathew C and Xiong, Guoming and Zhang, Wei and Yang, Rong and Cieplak, Piotr and Luo, Ray and Lee, Taisung and Caldwell, James and Wang, Junmei and Kollman, Peter}, title = {{A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations.}}, journal = {J. Comput. Chem.}, year = {2003}, volume = {24}, number = {16}, pages = {1999--2012}, annote = {reference for Amber 03} } @article{Marsh:2007jv, author = {Marsh, Derek}, title = {{Lateral Pressure Profile, Spontaneous Curvature Frustration, and the Incorporation and Conformation of Proteins in Membranes}}, journal = {Biophys. J.}, year = {2007}, volume = {93}, number = {11}, pages = {3884--3899}, month = dec } @article{Redfern:2007tk, author = {Redfern, O and Harrison, A and Dallman, T}, title = {{CATHEDRAL: a fast and effective algorithm to predict folds and domain boundaries from multidomain protein structures}}, journal = {PLoS {\ldots}}, year = {2007} } @article{ZEN:2008tz, author = {Zen, Andrea and Carnevale, Vincenzo and Lesk, Arthur M. and MICHELETTI, AND CRISTIAN}, title = {{SuppInfo: Correspondences between low-energy modes in enzymes: Dynamics-based alignment of enzymatic functional families}}, journal = {Protein Sci.}, year = {2008}, pages = {1--5} } @article{Hjermann:2009wy, author = {Hjermann, Dag {\O} and Bogstad, Bjarte and Dings{\o}r, Gjert Endre and Gj{\o}s{\ae}ter, Harald and Ottersen, Geir and Eikeset, Anne Maria and Stenseth, Nils Christian}, title = {{Trophic interactions affecting a key ecosystem component: a multi-stage analysis of the recruitment of the Barents Sea capelin}}, journal = {10 s.}, year = {2009} } @article{Cheng:wr, author = {Cheng, Jiongjia and Goldstein, Rebecca and Gershenson, Anne and Stec, Boguslaw and Roberts, Mary F}, title = {{The Cation-$\pi$ Box Is a Specific Phosphatidylcholine Membrane Targeting Motif}}, journal = {jbc.org}, year = {2013} } @article{Garcia:1992wh, author = {Garc{\'\i}a, AE}, title = {{Large-amplitude nonlinear motions in proteins.}}, journal = {Phys. Rev. Lett.}, year = {1992}, volume = {68}, number = {17}, pages = {2696--2699}, month = apr } @article{Pinheiro:1994hs, author = {Pinheiro, T J T}, title = {{The interaction of horse heart cytochrome c with phospholipid bilayers. Structural and dynamic effects}}, journal = {Biochimie}, year = {1994}, volume = {76}, number = {6}, pages = {489--500}, month = jan } @article{Sodt:2014bi, author = {Sodt, Alexander J and Pastor, Richard W}, title = {{Molecular Modeling of Lipid Membrane Curvature Induction by a Peptide: More than Simply Shape}}, journal = {Biophys. J.}, year = {2014}, volume = {106}, number = {9}, pages = {1958--1969}, month = may } @article{HOPKINS:1991gkb, author = {HOPKINS, C C E and NILSSEN, E M}, title = {{The rise and fall of the Barents Sea capelin (Mallotus villosus): a multivariate scenario}}, journal = {Polar Research}, year = {1991}, volume = {10}, number = {2}, pages = {535--546}, month = dec } @article{Hirst:2004jg, author = {Hirst, David and Aanes, Sondre and Storvik, Geir and Huseby, Ragnar Bang and Tvete, Ingunn Fride}, title = {{Estimating catch at age from market sampling data by using a Bayesian hierarchical model}}, journal = {Journal of the Royal Statistical Society: Series C (Applied Statistics)}, year = {2004}, volume = {53}, number = {1}, pages = {1--14}, month = jan } @article{Wall:2014hl, author = {Wall, Michael E and Adams, Paul D and Fraser, James S and Sauter, Nicholas K}, title = {{Diffuse X-Ray Scattering to Model Protein Motions}}, journal = {Structure}, year = {2014}, volume = {22}, number = {2}, pages = {182--184}, month = feb } @article{Zhou:2010eg, author = {Zhou, Huan-Xiang}, title = {{Rate theories for biologists}}, journal = {Quart. Rev. Biophys.}, year = {2010}, volume = {43}, number = {02}, pages = {219--293}, month = aug } @article{Anonymous:vr2dt-Sw, title = {{ess}}, year = {2007}, pages = {3}, month = apr } @webpage{Anonymous:kxVBnE4v, title = {{9472_Alternative%20Models%20of%20Ownership%20all_v4.pdf}}, url = {http://www.labour.org.uk/page/-/PDFs/9472_Alternative%20Models%20of%20Ownership%20all_v4.pdf} } @article{Verhey:2011hz, author = {Verhey, Kristen J and Kaul, Neha and Soppina, Virupakshi}, title = {{Kinesin Assembly and Movement in Cells}}, journal = {Annu. Rev. Biophys.}, year = {2011}, volume = {40}, number = {1}, pages = {267--288}, month = jun } @article{Carnevale:uPT2G0RE, author = {Carnevale, Vincenzo and Raugei, Simone and Micheletti, Cristian and Carloni, Paolo}, title = {{Convergent dynamics in the protease enzymatic superfamily.}}, journal = {JACS}, year = {2006}, volume = {128}, number = {30}, pages = {9766--9772}, month = aug } @article{Hajjar:2008gd, author = {Hajjar, Eric and Mihajlovic, Maja and Witko-Sarsat, Veronique and Lazaridis, Themis and Reuter, Nathalie}, title = {{Computational prediction of the binding site of proteinase 3 to the plasma membrane}}, journal = {Proteins: Struct., Funct., Bioinf.}, year = {2008}, volume = {71}, number = {4}, pages = {1655--1669} } @article{DiPaola:2012gm, author = {Di Paola, L and De Ruvo, M and Paci, P and Santoni, D and Giuliani, A}, title = {{Protein Contact Networks: An Emerging Paradigm in Chemistry}}, journal = {Chem. Rev}, year = {2012}, pages = {121127103808002}, month = nov } @article{PODonoghue:2003te, author = {PO'Donoghue and Luthey-Schulten, Z}, title = {{On the evolution of structure in aminoacyl-tRNA synthetases}}, journal = {Microbiology and molecular biology reviews}, year = {2003} } @article{Lemak:2014kx, author = {Lemak, Alexander and Wu, Bin and Yee, Adelinda and Houliston, Scott and Lee, Hsiau-Wei and Gutmanas, Aleksandras and Fang, Xianyang and Garcia, Maite and Semesi, Anthony and Wang, Yun-Xing and Prestegard, James H and Arrowsmith, Cheryl H}, title = {{Structural Characterization of a Flexible Two-Domain Protein in Solution Using Small Angle X-Ray Scattering and NMR Data}}, journal = {Structure}, year = {2014}, volume = {22}, number = {12}, pages = {1862--1874}, month = dec } @article{BRETSCHER:1972bq, author = {BRETSCHER, MARK S}, title = {{Asymmetrical Lipid Bilayer Structure for Biological Membranes}}, journal = {Nature}, year = {1972}, volume = {236}, number = {61}, pages = {11--12}, month = mar } @article{Liu:2012em, author = {Liu, Y and Bahar, I}, title = {{Sequence Evolution Correlates with Structural Dynamics}}, journal = {Molecular Biology and Evolution}, year = {2012}, volume = {29}, number = {9}, pages = {2253--2263}, month = aug } @article{Tirion:1996uf, author = {Tirion, Monique M}, title = {{Large amplitude elastic motions in proteins from a single-parameter, atomic analysis}}, journal = {Phys. Rev. Lett.}, year = {1996}, volume = {77}, number = {9}, pages = {1905--1908}, month = aug } @article{Dryga:wt, author = {Dryga, Anatoly and Chakrabarty, Suman and Vicatos, Spyridon and Warshel, Arieh}, title = {{Realistic simulation of the activation of voltage-gated ion channels}}, journal = {pnas.org} } @article{Mintseris:2005hg, author = {Mintseris, Julian and Wiehe, Kevin and Pierce, Brian and Anderson, Robert and Chen, Rong and Janin, Jo{\"e}l and Weng, Zhiping}, title = {{Protein-protein docking benchmark 2.0: An update}}, journal = {Proteins: Struct., Funct., Bioinf.}, year = {2005}, volume = {60}, number = {2}, pages = {214--216}, month = jun } @article{Phillips:2005gn, author = {Phillips, L Revell and Milescu, Mirela and Li-Smerin, Yingying and Mindell, Joseph A and Kim, Jae Il and Swartz, Kenton J}, title = {{Voltage-sensor activation with a tarantula toxin as cargo.}}, journal = {Nature}, year = {2005}, volume = {436}, number = {7052}, pages = {857--860}, month = aug } @article{McIntyre:2016gk, author = {McIntyre, Peter B and Liermann, Catherine A Reidy and Revenga, Carmen}, title = {{Linking freshwater fishery management to global food security and biodiversity conservation}}, journal = {Proc. Natl. Acad. Sci. U. S. A.}, year = {2016}, volume = {113}, number = {45}, pages = {12880--12885}, month = nov } @article{Mu:2004kr, author = {Mu, Yuguang and Nguyen, Phuong H and Stock, Gerhard}, title = {{Energy landscape of a small peptide revealed by dihedral angle principal component analysis}}, journal = {Proteins: Struct., Funct., Bioinf.}, year = {2004}, volume = {58}, number = {1}, pages = {45--52}, month = nov } @article{Hill:2012jz, author = {Hill, Krista K and Roemer, Sarah C and Churchill, Mair E A and Edwards, Dean P}, title = {{Structural and functional analysis of domains of the progesterone receptor}}, journal = {Molecular and Cellular Endocrinology}, year = {2012}, volume = {348}, number = {2}, pages = {418--429}, month = jan } @article{Korkmaz:2007gy, author = {Korkmaz, Brice and Hajjar, Eric and Kalupov, Timofey and Reuter, Nathalie and Brillard-Bourdet, Michele and Moreau, Thierry and Juliano, Luiz and Gauthier, Francis}, title = {{Influence of charge distribution at the active site surface on the substrate specificity of human neutrophil protease 3 and elastase - A kinetic and molecular modeling analysis}}, journal = {J. Biol. Chem.}, year = {2007}, volume = {282}, number = {3}, pages = {1989--1997} } @incollection{Maier:2005fx, author = {Maier, Claudia S and Deinzer, Max L}, title = {{Protein Conformations, Interactions, and H/D Exchange}}, year = {2005}, pages = {312--360}, publisher = {Elsevier} } @article{Lee:2013gk, author = {Lee, Jong Kook and Gopal, Ramamourthy and Park, Seong-Cheol and Ko, Hyun Sook and Kim, Yangmee and Hahm, Kyung-Soo and Park, Yoonkyung}, title = {{A Proline-Hinge Alters the Characteristics of the Amphipathic $\alpha$-helical AMPs}}, journal = {PLoS ONE}, year = {2013}, volume = {8}, number = {7}, pages = {e67597}, month = jul } @article{Volstad:2011gb, author = {Volstad, J H and Korsbrekke, K and Nedreaas, K H and Nilsen, M and Nilsson, G N and Pennington, M and Subbey, S and Wienerroither, R}, title = {{Probability-based surveying using self-sampling to estimate catch and effort in Norway's coastal tourist fishery}}, journal = {ICES Journal of Marine Science}, year = {2011}, volume = {68}, number = {8}, pages = {1785--1791}, month = aug } @article{Aglen:2014wt, author = {Aglen, A F}, title = {{Den selvstendige betydningen til designloven {\textsection} 8, 1. ledd, nr. 1 som avgresning mellom design- og patentretten. Hva skal til for at noe }}, year = {2014} } @article{Block:2006gc, author = {Block, Peter and Paern, Juri and H{\"u}llermeier, Eyke and Sanschagrin, Paul and Sotriffer, Christoph A and Klebe, Gerhard}, title = {{Physicochemical descriptors to discriminate protein-protein interactions in permanent and transient complexes selected by means of machine learning algorithms}}, journal = {Proteins: Struct., Funct., Bioinf.}, year = {2006}, volume = {65}, number = {3}, pages = {607--622}, month = nov } @article{TothPetroczy:wk, author = {T{\'o}th-Petr{\'o}czy, {\'A}gnes and Tawfik, Dan S}, title = {{Slow protein evolutionary rates are dictated by surface{\textendash}core association}} } @article{Hinsen:2000we, author = {Hinsen, Konrad and Petrescu, Andrei-Jose and Dellerue, Serge and Bellissent-Funel, Marie-Caire and Kneller, Gerald R}, title = {{Harmonicity in slow protein dynamics}}, journal = {Chem. Phys.}, year = {2000}, volume = {261}, number = {1-2}, pages = {25--37} } @article{Wrabl:2011bk, author = {Wrabl, James O and Gu, Jenny and Liu, Tong and Schrank, Travis P and Whitten, Steven T and Hilser, Vincent J}, title = {{The role of protein conformational fluctuations in allostery, function, and evolution}}, journal = {Biophys. Chem.}, year = {2011}, volume = {159}, number = {1}, pages = {129--141}, month = nov } @article{Lu:2005ic, author = {Lu, Nick Z and Cidlowski, John A}, title = {{Translational regulatory mechanisms generate N-terminal glucocorticoid receptor isoforms with unique transcriptional target genes.}}, journal = {Mol. Cell}, year = {2005}, volume = {18}, number = {3}, pages = {331--342}, month = apr } @article{Delarue:2002wx, author = {Delarue, M and Sanejouand, Y-H}, title = {{Simplified normal mode analysis of conformational transitions in DNA-dependent polymerases: the elastic network model.}}, journal = {J. Mol. Biol.}, year = {2002}, volume = {320}, number = {5}, pages = {1011--1024}, month = jul } @webpage{Anonymous:LVeFSr1x, title = {{19313.full.pdf}}, url = {http://www.pnas.org/content/110/48/19313.full.pdf} } @article{Mondal:2014hi, author = {Mondal, Jagannath and Friesner, Richard A and Berne, Bruce J}, title = {{Role of desolvation in thermodynamics and kinetics of ligand binding to a kinase}}, journal = {J Chem Theory Comput}, year = {2014}, pages = {141113153931002}, month = nov } @article{Dovi:1991fe, author = {Dov{\`\i}, V G and Paladino, O and Reverberi, A P}, title = {{Some remarks on the use of the inverse hessian matrix of the likelihood function in the estimation of statistical properties of parameters}}, journal = {Applied Mathematics Letters}, year = {1991}, volume = {4}, number = {1}, pages = {87--90}, month = jan } @article{Ruschhaup:2004ut, author = {Ruschhaup, Markus and Huber, Wolfgang and Poustka, Annemarie and Mansmann, Ulrich}, title = {{A Compendium to Ensure Computational Reproducibility in High-Dimensional Classification Tasks }}, year = {2004}, pages = {1--26}, month = dec } @article{Lazaridis:2003wu, author = {Lazaridis, T}, title = {{Effective energy function for proteins in lipid membranes - Lazaridis - 2003 - Proteins: Structure, Function, and Bioinformatics - Wiley Online Library}}, journal = {Proteins: Structure}, year = {2003} } @article{Anderluh:2005kk, author = {Anderluh, Gregor and Razpotnik, Andrej and Podlesek, Zdravko and Macek, Peter and Separovic, Frances and Norton, Raymond S}, title = {{Interaction of the eukaryotic pore-forming cytolysin equinatoxin II with model membranes: 19F NMR studies.}}, journal = {J. Mol. Biol.}, year = {2005}, volume = {347}, number = {1}, pages = {27--39}, month = mar } @article{Inaba:2016cb, author = {Inaba, Takehiko and Kishimoto, Takuma and Murate, Motohide and Tajima, Takuya and Sakai, Shota and Abe, Mitsuhiro and Makino, Asami and Tomishige, Nario and Ishitsuka, Reiko and Ikeda, Yasuo and Takeoka, Shinji and Kobayashi, Toshihide}, title = {{Phospholipase C$\beta$1 induces membrane tubulation and is involved in caveolae formation.}}, journal = {Proc. Natl. Acad. Sci. U. S. A.}, year = {2016}, volume = {113}, number = {28}, pages = {7834--7839}, month = jul } @article{Baldwin:1979wr, author = {Baldwin, Joyce and Chothia, Cyrus}, title = {{Haemoglobin: the structural changes related to ligand binding and its allosteric mechanism.}}, journal = {J. Mol. Biol.}, year = {1979}, volume = {129}, number = {2}, pages = {175--220}, month = apr } @article{LindorffLarsen:2012js, author = {Lindorff-Larsen, Kresten and Maragakis, Paul and Piana, Stefano and Eastwood, Michael P and Dror, Ron O and Shaw, David E}, title = {{Systematic Validation of Protein Force Fields against Experimental Data}}, journal = {PLoS ONE}, year = {2012}, volume = {7}, number = {2}, pages = {e32131}, month = feb } @article{Micheletti:2012hb, author = {Micheletti, Cristian}, title = {{Comparing proteins by their internal dynamics: Exploring structure{\textendash}function relationships beyond static structural alignments}}, journal = {Physics of Life Reviews}, year = {2012}, month = oct } @article{Stansfeld:2015kg, author = {Stansfeld, Phillip J and Goose, Joseph E and Caffrey, Martin and Carpenter, Elisabeth P and Parker, Joanne L and Newstead, Simon and Sansom, Mark S P}, title = {{MemProtMD: Automated Insertion of Membrane Protein Structures into Explicit Lipid Membranes}}, journal = {Structure}, year = {2015}, volume = {23}, number = {7}, pages = {1350--1361}, month = jul } @article{Feibelman:2015wg, author = {Feibelman, Peter J}, title = {{A PhD is not enough!}}, year = {2015}, pages = {1--165}, month = sep } @article{COHEN:1968ub, author = {COHEN, J}, title = {{WEIGHTED KAPPA - NOMINAL SCALE AGREEMENT WITH PROVISION FOR SCALED DISAGREEMENT OR PARTIAL CREDIT}}, journal = {Psychol Bull}, year = {1968}, volume = {70}, number = {4}, pages = {213--{\&}} } @article{Motlagh:2012bk, author = {Motlagh, Hesam N and Li, Jing and Thompson, E Brad and Hilser, Vincent J}, title = {{Interplay between allostery and intrinsic disorder in an ensemble.}}, journal = {Biochem. Soc. Trans.}, year = {2012}, volume = {40}, number = {5}, pages = {975--980}, month = oct } @article{Schrank:2011df, author = {Schrank, Travis P and Elam, W Austin and Li, Jing and Hilser, Vincent J}, title = {{Strategies for the thermodynamic characterization of linked binding/local folding reactions within the native state application to the LID domain of adenylate kinase from Escherichia coli.}}, journal = {Meth. Enzymol.}, year = {2011}, volume = {492}, pages = {253--282} } @article{Geman:2016kn, author = {Geman, Donald and Geman, Stuart}, title = {{Opinion: Science in the age of selfies}}, journal = {Proc. Natl. Acad. Sci. U. S. A.}, year = {2016}, volume = {113}, number = {34}, pages = {9384--9387}, month = aug } @article{Papaleo:2009vw, author = {Papaleo, E and Mereghetti, P and Fantucci, P and Grandori, R and De Gioia, L}, title = {{Free-energy landscape, principal component analysis, and structural clustering to identify representative conformations from molecular dynamics simulations: The myoglobin case}}, journal = {Journal of Molecular Graphics and Modelling}, year = {2009}, volume = {27}, number = {8}, pages = {889--899} } @article{Anonymous:6B3gAR2B, author = {von Ahn, Luis and Dabbish, Laura}, title = {{Labeling Images with a Computer Game}}, year = {2004}, pages = {1--8}, month = jan } @article{Fawcett:2006vn, author = {Fawcett, T}, title = {{ScienceDirect - Pattern Recognition Letters : An introduction to ROC analysis}}, journal = {Pattern recognition letters}, year = {2006} } @article{Hinsen:2013df, author = {Hinsen, Konrad and Hu, Shuangwei and Kneller, Gerald R and Niemi, Antti J}, title = {{A comparison of reduced coordinate sets for describing protein structure}}, journal = {J. Chem. Phys.}, year = {2013}, volume = {139}, number = {12}, pages = {124115} } @article{Denning:2011wj, author = {Denning, Peter J}, title = {{The Great Principles of Computing}}, journal = {American Scientist}, year = {2011}, pages = {1--8}, month = apr } @article{TonddastNavaei:2015bm, author = {Tonddast-Navaei, Sam and Skolnick, Jeffrey}, title = {{Are protein-protein interfaces special regions on a protein{\textquoteright}s surface?}}, journal = {J. Chem. Phys.}, year = {2015}, volume = {143}, number = {24}, pages = {243149}, month = dec } @article{Teilum:2009bfa, author = {Teilum, Kaare and Olsen, Johan G and Kragelund, Birthe B}, title = {{Functional aspects of protein flexibility}}, journal = {Cell Mol Life Sci}, year = {2009}, volume = {66}, number = {14}, pages = {2231--2247}, month = mar } @article{Hinsen:1998we, author = {Hinsen, Konrad}, title = {{Analysis of domain motions by approximate normal mode calculations}}, journal = {Proteins: Struct., Funct., Bioinf.}, year = {1998}, volume = {33}, number = {3}, pages = {417--429} } @article{Spielman:2004vw, author = {Spielman, D and Teng, S}, title = {{Smoothed analysis of algorithms: Why the simplex algorithm usually takes polynomial time}}, journal = {Journal of the ACM (JACM)}, year = {2004} } @article{Hjermann:2010cm, author = {Hjermann, Dag {\O}ysteinHjermannD {\O} and Bogstad, BjarteBogstadB and Dings{\o}r, Gjert EndreDings{\o}rG E and Gj{\o}s{\ae}ter, HaraldGj{\o}s{\ae}terH and Ottersen, GeirOttersenG and Eikeset, Anne MariaEikesetA M and Stenseth, Nils ChristianStensethN C}, title = {{Trophic interactions affecting a key ecosystem component: a multistage analysis of the recruitment of the Barents Sea capelin (Mallotus villosus)}}, journal = {Canadian Journal of Fisheries and Aquatic Sciences}, year = {2010}, volume = {67}, number = {9}, pages = {1363--1375}, month = aug } @article{Cumming:2007du, author = {Cumming, G and Fidler, F and Vaux, D L}, title = {{Error bars in experimental biology}}, journal = {The Journal of Cell Biology}, year = {2007}, volume = {177}, number = {1}, pages = {7--11}, month = apr } @webpage{Anonymous:DksxMc3G, title = {{A natural unification of GNM and ANM and the role of inter-residue forces - Abstract - Physical Biology - IOPscience}}, url = {http://iopscience.iop.org/1478-3975/11/3/036002} } @article{Bakhtiarizadeh:2014cr, author = {Bakhtiarizadeh, Mohammad Reza and Moradi-Shahrbabak, Mohammad and Ebrahimi, Mansour and Ebrahimie, Esmaeil}, title = {{Neural network and SVM classifiers accurately predict lipid binding proteins, irrespective of sequence homology}}, journal = {Journal of Theoretical Biology}, year = {2014}, volume = {356}, pages = {213--222}, month = sep } @article{Hinsen:2010cx, author = {Hinsen, Konrad}, title = {{Computer code: incentives needed}}, journal = {Nature}, year = {2010}, volume = {468}, number = {7320}, pages = {37--37}, month = nov } @article{Ryckaert:1977gp, author = {Ryckaert, Jean-Paul and Ciccotti, Giovanni and Berendsen, Herman JC}, title = {{Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes}}, journal = {J Comput Phys}, year = {1977}, volume = {23}, number = {3}, pages = {327--341}, month = feb } @article{Miyashita:2011jb, author = {Miyashita, O and ONUCHIC, J N and WOLYNES, P G}, title = {{Nonlinear elasticity, proteinquakes, and the energy landscapes of functional transitions in proteins}}, journal = {Proc. Natl. Acad. Sci. U. S. A.}, year = {2011}, volume = {100}, number = {22}, pages = {12570--12575}, month = may } @article{Wan:2016jk, author = {Wan, Ruixue and Yan, Chuangye and Bai, Rui and Wang, Lin and Huang, Min and Wong, Catherine C L and Shi, Yigong}, title = {{The 3.8 {\AA} structure of the U4/U6.U5 tri-snRNP: Insights into spliceosome assembly and catalysis.}}, journal = {Science}, year = {2016}, month = jan } @article{Matsuoka:2013jp, author = {Matsuoka, Satomi and Shibata, Tatsuo and Ueda, Masahiro}, title = {{Asymmetric PTEN Distribution Regulated by Spatial Heterogeneity in Membrane-Binding State Transitions}}, journal = {PLoS Comput. Biol.}, year = {2013}, volume = {9}, number = {1}, pages = {e1002862}, month = jan } @article{Pingali:2016et, author = {Pingali, Prabhu L}, title = {{Opinion: The hunger metrics mirage: There{\textquoteright}s been less progress on hunger reduction than it appears}}, journal = {Proc. Natl. Acad. Sci. U. S. A.}, year = {2016}, volume = {113}, number = {18}, pages = {4880--4883}, month = may } @article{Lawley:1963uh, author = {Lawley, D}, title = {{On Testing a Set of Correlation Coefficients for Equality}}, journal = {The Annals of Mathematical Statistics}, year = {1963}, volume = {34}, number = {1}, pages = {149--151}, month = mar } @article{Ghysels:2010cp, author = {Ghysels, An and Van Speybroeck, Veronique and Pauwels, Ewald and Catak, Saron and Brooks, Bernard R and Van Neck, Dimitri and Waroquier, Michel}, title = {{Comparative Study of Various Normal Mode Analysis Techniques Based on Partial Hessians}}, journal = {J. Comput. Chem.}, year = {2010}, volume = {31}, number = {5}, pages = {994--1007} } @article{Touw:2015ff, author = {Touw, W G and Baakman, C and Black, J and te Beek, T A H and Krieger, E and Joosten, R P and VRIEND, G}, title = {{A series of PDB-related databanks for everyday needs}}, journal = {Nucleic Acids Res.}, year = {2015}, volume = {43}, number = {D1}, pages = {D364--D368}, month = jan } @unpublished{Fuglebakk:2013vv, author = {Fuglebakk, Edvin and Tiwari, Sandhya and Hollup, Siv Midtun and Cragnolini, Tristan and Skjaerven, Lars and Grindhaug, Svenn Helge and Kidane, Tekle and Reuter, Nathalie}, title = {{Comparing protein structure flexibility using WEBnm@ v2.0}} } @article{Yang:2009wg, author = {Yang, L and Song, G and Jernigan, RL}, title = {{Protein elastic network models and the ranges of cooperativity}}, journal = {Proc. Natl. Acad. Sci. U. S. A.}, year = {2009}, volume = {106}, number = {30}, pages = {12347--12352}, month = jul } @article{Anonymous:qyhV4jDe, title = {{Common Principal Components}}, year = {2010}, pages = {1--14}, month = mar } @article{Kallberg:2012cw, author = {Kallberg, M and Bhardwaj, N and Langlois, R and Lu, H}, title = {{A structure-based protocol for learning the family-specific mechanisms of membrane-binding domains}}, journal = {Bioinformatics}, year = {2012}, volume = {28}, number = {18}, pages = {i431--i437}, month = sep } @article{Irback:uh, author = {Irback, Anders and Mitternacht, Simon}, title = {{Protein Aggregation and Unfolding Studied Using an All-Atom Model with a Simplified Energy Function}}, pages = {15} } @article{Misra:1999uo, author = {Misra, S and Hurley, J H}, title = {{Crystal structure of a phosphatidylinositol 3-phosphate-specific membrane-targeting motif, the FYVE domain of Vps27p.}}, journal = {Cell}, year = {1999}, volume = {97}, number = {5}, pages = {657--666}, month = may } @article{Ennaceur:2009hk, author = {Ennaceur, Sue M and Hicks, Matthew R and Pridmore, Catherine J and Dafforn, Tim R and Rodger, Alison and Sanderson, John M}, title = {{Peptide Adsorption to Lipid Bilayers: Slow Processes Revealed by Linear Dichroism Spectroscopy}}, journal = {Biophys. J.}, year = {2009}, volume = {96}, number = {4}, pages = {1399--1407}, month = feb } @article{Wimley:1996vpa, author = {Wimley, W C and White, S H}, title = {{Experimentally determined hydrophobicity scale for proteins at membrane interfaces.}}, journal = {Nat. Struct Biol.}, year = {1996}, volume = {3}, number = {10}, pages = {842--848}, month = oct } @article{Weber:2015dn, author = {Weber, Daniel K and Yao, Shenggen and Rojko, Nejc and Anderluh, Gregor and Lybrand, Terry P and Downton, Matthew T and Wagner, John and Separovic, Frances}, title = {{Characterization of the Lipid-Binding Site of Equinatoxin II by NMR and Molecular Dynamics Simulation}}, journal = {Biophysj}, year = {2015}, volume = {108}, number = {8}, pages = {1987--1996}, month = apr } @article{Meyer:2010wp, author = {Meyer, T and D'Abramo, M}, title = {{MoDEL (Molecular Dynamics Extended Library): A Database of Atomistic Molecular Dynamics Trajectories}}, journal = {Structure}, year = {2010} } @article{Calandrini:2008im, author = {Calandrini, V and Hamon, V and Hinsen, K and Calligari, P and Bellissent-Funel, M C and Kneller, G R}, title = {{Relaxation dynamics of lysozyme in solution under pressure: Combining molecular dynamics simulations and quasielastic neutron scattering}}, journal = {Chem. Phys.}, year = {2008}, volume = {345}, number = {2-3}, pages = {289--297}, month = apr } @article{Echave:2012ef, author = {Echave, Juli{\'a}n}, title = {{Why are the low-energy protein normal modes evolutionarily conserved?}}, journal = {Pure Appl. Chem.}, year = {2012}, volume = {84}, number = {9}, pages = {1931--1937} } @article{Ellis:2016ek, author = {Ellis, J R and McCully Phillips, S R and Poisson, F}, title = {{A review of capture and post-release mortality of elasmobranchs}}, journal = {J Fish Biol}, year = {2016}, volume = {90}, number = {3}, pages = {653--722}, month = nov } @article{Wrabl:2008wn, author = {Wrabl, James O and Grishin, Nick V}, title = {{Statistics of Random Protein Superpositions p-values for Pairwise Structure Alignment}}, journal = {Jorunal of Computational Biology}, year = {2008}, volume = {15}, number = {3}, pages = {317--355} } @article{Palazzo:2010fs, author = {Palazzo, David J and Warnakulasooriya, Rasil and Pritchard, David E}, title = {{Patterns, correlates, and reduction of homework copying}}, journal = {Phys. Rev. ST Phys. Educ. Res.}, year = {2010}, volume = {6}, number = {1}, pages = {010104}, month = mar } @article{Vanni:2014gm, author = {Vanni, Stefano and Hirose, Hisaaki and Barelli, H eacute l egrave ne and Gautier, Romain and Antonny, Bruno}, title = {{A sub-nanometre view of how membrane curvature and composition modulate lipid packing and protein recruitment}}, journal = {Nature Communications}, year = {2014}, volume = {5}, pages = {1--10}, month = sep } @webpage{Anonymous:C-KvVQxl, title = {{Verification Required}}, url = {http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.90.075502} } @article{Hinsen:2007ir, author = {Hinsen, Konrad}, title = {{Structural flexibility in proteins: impact of the crystal environment}}, journal = {Bioinformatics}, year = {2008}, volume = {24}, number = {4}, pages = {521--528} } @article{Pearce:2010fo, author = {Pearce, Laura R and Komander, David and Alessi, Dario R}, title = {{The nuts and bolts of AGC protein kinases}}, journal = {Nat Rev Mol Cell Biol}, year = {2010}, volume = {11}, number = {1}, pages = {9--22}, month = jan } @article{Maguid:2008gj, author = {Maguid, Sandra and Fern{\'a}ndez-Alberti, Sebasti{\'a}n and Echave, Juli{\'a}n}, title = {{Evolutionary conservation of protein vibrational dynamics}}, journal = {Gene}, year = {2008}, volume = {422}, number = {1-2}, pages = {7--13}, month = oct } @article{Petre:2013uo, author = {Petre, Marian and Wilson, Greg}, title = {{PLOS/Mozilla Scientific Code Review Pilot: Summary of Findings}}, year = {2013}, month = nov } @article{Ashley:2015gs, author = {Ashley, Steven}, title = {{Core Concept: Ergodic theory plays a key role in multiple fields:}}, journal = {Proc. Natl. Acad. Sci. U. S. A.}, year = {2015}, pages = {1914--1914}, month = feb } @article{McLaughlin:2005gp, author = {McLaughlin, Stuart and Murray, Diana}, title = {{Plasma membrane phosphoinositide organization by protein electrostatics}}, journal = {Nature}, year = {2005}, volume = {438}, number = {7068}, pages = {605--611}, month = dec } @article{Broecker:wv, author = {Broecker, Jana and Fiedler, Sebastian and Gimpl, Katharina and Keller, Sandro}, title = {{Polar interactions trump hydrophobicity in stabilizing the self-inserting membrane protein Mistic.}}, journal = {JACS}, year = {2014}, volume = {136}, number = {39}, pages = {13761--13768}, month = oct } @article{Englander:2014et, author = {Englander, S W and Mayne, L}, title = {{The nature of protein folding pathways}}, journal = {Proc. Natl. Acad. Sci. U. S. A.}, year = {2014}, volume = {111}, number = {45}, pages = {15873--15880}, month = nov } @article{JordanLScott:2012bl, author = {Jordan L Scott, Catherine A Musselman Emmanuel Adu-Gyamfi Tatiana G Kutateladze Robert V Stahelin}, title = {{Emerging methodologies to investigate lipid{\textendash}protein interactions}}, journal = {Integrative biology : quantitative biosciences from nano to macro}, year = {2012}, volume = {4}, number = {3}, pages = {247}, month = mar } @article{Orozco:2014ej, author = {Orozco, Modesto}, title = {{A theoretical view of protein dynamics}}, journal = {Chem. Soc. Rev.}, year = {2014}, volume = {43}, number = {14}, pages = {5051} } @webpage{Anonymous:bMXqAkKj, title = {{PLOS Computational Biology: Exploring the Conformational Transitions of Biomolecular Systems Using a Simple Two-State Anisotropic Network Model}}, url = {http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003521} } @article{Eichinger:1978ey, author = {Eichinger, B E}, title = {{Scattering Functions for Gaussian Molecules}}, journal = {Macromolecules}, year = {1978}, volume = {11}, number = {2}, pages = {432--433}, month = mar } @article{Seckler:2013cf, author = {Seckler, James M and Miao, Hongyu and Grossfield, Alan M}, title = {{A Structural and Dynamics Survey of HIV-1 Reverse Transcriptase}}, journal = {Biophys. J.}, year = {2013}, volume = {104}, number = {2}, pages = {57a}, month = jan } @article{Wimley:1996bv, author = {Wimley, William C and Creamer, Trevor P and White, Stephen H}, title = {{Solvation Energies of Amino Acid Side Chains and Backbone in a Family of Host{\textminus}Guest Pentapeptides {\dag}}}, journal = {Biochemistry}, year = {1996}, volume = {35}, number = {16}, pages = {5109--5124}, month = jan } @article{Wall:wn, author = {Wall, Michael E and Van Benschoten, Andrew H and Sauter, Nicholas K and Adams, Paul D and Fraser, James S and Terwilliger, Thomas C}, title = {{Conformational dynamics of a crystalline protein from microsecond-scale molecular dynamics simulations and diffuse X-ray scattering}}, journal = {pnas.org} } @article{Anonymous:-DHHWTqF, title = {{assignment}}, year = {2005}, pages = {6} } @article{Wako:2011eh, author = {Wako, Hiroshi and Endo, Shigeru}, title = {{Ligand-induced conformational change of a protein reproduced by a linear combination of displacement vectors obtained from normal mode analysis.}}, journal = {Biophys. Chem.}, year = {2011}, volume = {159}, number = {2-3}, pages = {257--266} } @article{East:2016ck, author = {East, Alexandra and Mechaly, Ariel E and Huysmans, Gerard H M and Bernarde, C{\'e}dric and Tello-Manigne, Diana and Nadeau, Nathalie and Pugsley, Anthony P and Buschiazzo, Alejandro and Alzari, Pedro M and Bond, Peter J and Francetic, Olivera}, title = {{Structural Basis of Pullulanase Membrane Binding and Secretion Revealed by X-Ray Crystallography, Molecular Dynamics and Biochemical Analysis}}, journal = {Structure}, year = {2016}, volume = {24}, number = {1}, pages = {92--104}, month = jan } @article{Goldfine:1984vi, author = {Goldfine, H}, title = {{Bacterial membranes and lipid packing theory.}}, journal = {Journal of lipid research}, year = {1984} } @article{Adcock:2006il, author = {Adcock, Stewart A. and McCammon, J Andrew}, title = {{Molecular dynamics: Survey of methods for simulating the activity of proteins}}, journal = {Chem. Rev}, year = {2006}, volume = {106}, number = {5}, pages = {1589--1615} } @article{Yau:1998gp, author = {Yau, W M and Wimley, W C and Gawrisch, K and White, S H}, title = {{The preference of tryptophan for membrane interfaces.}}, journal = {Biochemistry}, year = {1998}, volume = {37}, number = {42}, pages = {14713--14718}, month = oct } @book{Pahl:2001co, author = {Pahl, Matthew C and Askinazi, Olga L and Hamilton, Catherine and Cheng, Irene and Cichewicz, Karol and Kuhn, Jason and Manohar, Sumanth and Deppmann, Christopher D}, title = {{Signalling via Single-Pass Transmembrane Proteins}}, publisher = {John Wiley {\&} Sons, Ltd}, year = {2001}, address = {Chichester, UK}, month = may } @article{Hayward:2011th, author = {Hayward, Steven and DeGroot, BL}, title = {{Normal Modes and Essential Dynamics}}, year = {2011}, pages = {1--18}, month = aug } @article{Bartocci:2016jr, author = {Bartocci, Ezio and Pietro Li{\'o}}, title = {{Computational Modeling, Formal Analysis, and Tools for Systems Biology}}, journal = {PLoS Comput. Biol.}, year = {2016}, volume = {12}, number = {1}, pages = {e1004591}, month = jan } @article{Hinsen:2000wia, author = {Hinsen, K}, title = {{The molecular modeling toolkit: A new approach to molecular simulations}}, journal = {J. Comput. Chem.}, year = {2000}, volume = {21}, number = {2}, pages = {79--85} } @incollection{Kessel:2002ft, author = {Kessel, Amit and Ben-Tal, Nir}, title = {{Free energy determinants of peptide association with lipid bilayers}}, booktitle = {Current topics in membranes}, year = {2002}, pages = {205--253}, publisher = {Elsevier} } @article{vanderSpoel:2005hz, author = {van der Spoel, David and Lindahl, Erik and Hess, Berk and Groenhof, Gerrit and Mark, Alan E and Berendsen, Herman J C}, title = {{GROMACS: Fast, flexible, and free}}, journal = {J. Comput. Chem.}, year = {2005}, volume = {26}, number = {16}, pages = {1701--1718} } @article{Adamian:2011ds, author = {Adamian, Larisa and Naveed, Hammad and Liang, Jie}, title = {{Lipid-binding surfaces of membrane proteins: Evidence from evolutionary and structural analysis}}, journal = {Biochimica et Biophysica Acta (BBA) - Biomembranes}, year = {2011}, volume = {1808}, number = {4}, pages = {1092--1102}, month = apr } @article{Drin:2009in, author = {Drin, Guillaume and Antonny, Bruno}, title = {{Amphipathic helices and membrane curvature}}, journal = {Febs Lett}, year = {2009}, volume = {584}, number = {9}, pages = {1840--1847}, month = oct } @article{Marcos:2010bg, author = {Marcos, Enrique and Crehuet, Ramon and Bahar, Ivet}, title = {{On the conservation of the slow conformational dynamics within the amino acid kinase family: NAGK the paradigm}}, journal = {PLoS Comput. Biol.}, year = {2010}, volume = {6}, number = {4}, pages = {e1000738} } @article{Bhardwaj:2006hia, author = {Bhardwaj, Nitin and Stahelin, Robert V and Langlois, Robert E and Cho, Wonhwa and Lu, Hui}, title = {{Structural Bioinformatics Prediction of Membrane-binding Proteins}}, journal = {J. Mol. Biol.}, year = {2006}, volume = {359}, number = {2}, pages = {486--495}, month = jun } @article{Rosenberg:2017bm, author = {Rosenberg, Andrew A and Kleisner, Kristin M and Afflerbach, Jamie and Anderson, Sean C and Dickey-Collas, Mark and Cooper, Andrew B and Fogarty, Michael J and Fulton, Elizabeth A and Guti{\'e}rrez, Nicol{\'a}s L and Hyde, Kimberly J W and Jardim, Ernesto and Jensen, Olaf P and Kristiansen, Trond and Longo, Catherine and Minte-Vera, Carolina V and Minto, C{\'o}il{\'\i}n and Mosqueira, Iago and Osio, Giacomo Chato and Ovando, Daniel and Selig, Elizabeth R and Thorson, James T and Walsh, Jessica C and Ye, Yimin}, title = {{Applying a New Ensemble Approach to Estimating Stock Status of Marine Fisheries Around the World}}, journal = {CONSERVATION LETTERS}, year = {2017}, pages = {1--18}, month = mar } @article{Hilser:2011ec, author = {Hilser, V J and Thompson, E B}, title = {{Structural Dynamics, Intrinsic Disorder, and Allostery in Nuclear Receptors as Transcription Factors}}, journal = {J. Biol. Chem.}, year = {2011}, volume = {286}, number = {46}, pages = {39675--39682}, month = nov } @article{Sumandea:1999gh, author = {Sumandea, Marius and Das, Sudipto and Sumandea, Claudia and Cho, Wonhwa}, title = {{Roles of Aromatic Residues in High Interfacial Activity of Naja naja atraPhospholipase A 2{\dag}}}, journal = {Biochemistry}, year = {1999}, volume = {38}, number = {49}, pages = {16290--16297}, month = dec } @book{Anonymous:2010tn, title = {{apps.webofknowledge.com}}, publisher = {Springer New York}, year = {2010}, address = {New York, NY}, month = sep } @article{Sanderson:2012ex, author = {Sanderson, John M}, title = {{Resolving the kinetics of lipid, protein and peptide diffusion in membranes}}, journal = {Mol Membr Biol}, year = {2012}, volume = {29}, number = {5}, pages = {118--143}, month = aug } @article{Wang:2001jw, author = {Wang, Q J}, title = {{Role of Hydrophobic Residues in the C1b Domain of Protein Kinase C delta on Ligand and Phospholipid Interactions}}, journal = {J. Biol. Chem.}, year = {2001}, volume = {276}, number = {22}, pages = {19580--19587}, month = mar } @article{Kleinberg:2004vg, author = {Kleinberg, Jon and Papadimitriou, Christos}, title = {{Computability and Complexity}}, journal = {Computer Science}, year = {2004}, pages = {1--11} } @article{Ingolfsson:2014ei, author = {Ing{\'o}lfsson, Helgi I and Melo, Manuel N and van Eerden, Floris J and Arnarez, Cl{\'e}ment and Lopez, Cesar A and Wassenaar, Tsjerk A and Periole, Xavier and de Vries, Alex H and Tieleman, D Peter and Marrink, Siewert J}, title = {{Lipid Organization of the Plasma Membrane}}, journal = {JACS}, year = {2014}, volume = {136}, number = {41}, pages = {14554--14559}, month = oct } @article{Potestio:2010bl, author = {Potestio, R and Aleksiev, T and Pontiggia, F and Cozzini, S and Micheletti, C}, title = {{ALADYN: a web server for aligning proteins by matching their large-scale motion}}, journal = {Nucleic Acids Res.}, year = {2010}, volume = {38}, number = {Web Server}, pages = {W41--W45}, month = jul } @article{Nguyen:2005ch, author = {Nguyen, Leonard T and Schibli, David J and Vogel, Hans J}, title = {{Structural studies and model membrane interactions of two peptides derived from bovine lactoferricin}}, journal = {Journal of Peptide Science}, year = {2005}, volume = {11}, number = {7}, pages = {379--389} } @article{Wei:2014fk, author = {Wei, Hui and Mo, Jingjie and Tao, Li and Russell, Reb J and Tymiak, Adrienne A and Chen, Guodong and Iacob, Roxana E and Engen, John R}, title = {{Hydrogen/deuterium exchange mass spectrometry for probing higher order structure of protein therapeutics: methodology and applications}}, journal = {Drug Discovery Today}, year = {2014}, volume = {19}, number = {1}, pages = {95--102}, month = jan } @inproceedings{Zwanzig:NFh-9m1X, author = {Zwanzig, Robert W}, title = {{Statistical Mechanics of Irreversibility}}, booktitle = {unm.edu} } @article{Stahelin:2003cv, author = {Stahelin, Robert V and Burian, Aura and Bruzik, Karol S and Murray, Diana and Cho, Wonhwa}, title = {{Membrane Binding Mechanisms of the PX Domains of NADPH Oxidase p40 phox and p47 phox}}, journal = {jbc.org}, year = {2003}, volume = {278}, number = {16}, pages = {14469--14479}, month = apr } @article{Gjosaeter:1998uk, author = {Gjosaeter, H}, title = {{The population biology and exploitation of capelin (Mallotus villosus) in the Barents Sea}}, journal = {Sarsia}, year = {1998}, volume = {83}, number = {6}, pages = {453--496} } @article{Anderson:2006tg, author = {Anderson, R}, title = {{Simple equipment for Chladni pattern}}, journal = {Physics Education}, year = {2006} } @misc{aavenndiagram:nmU7Kerr, title = {{Venn diagram amino acids}}, month = mar, year = {2013} } @article{Karplus:2011vy, author = {Karplus, Martin}, title = {{Behind the folding funnel diagram (vol 7, pg 401, 2011)}}, journal = {Nat Chem Biol}, year = {2011}, volume = {7}, number = {9}, pages = {648--648} } @article{Martin:2005ela, author = {Martin, Andrew C. R.}, title = {{Mapping PDB chains to UniProtKB entries}}, journal = {Bioinformatics}, year = {2005}, volume = {21}, number = {23}, pages = {4297--4301} } @article{Lai:2012gq, author = {Lai, Jason and Jin, Jing and Kubelka, Jan and Liberles, David A}, title = {{A phylogenetic analysis of normal modes evolution in enzymes and its relationship to enzyme function}}, journal = {J. Mol. Biol.}, year = {2012}, pages = {1--55}, month = may } @article{Anonymous:vS6QApXi, title = {{matching}}, year = {2007}, pages = {10} } @article{Pogozheva:2013ei, author = {Pogozheva, Irina D and Tristram-Nagle, Stephanie and Mosberg, Henry I and Lomize, Andrei L}, title = {{Biochimica et Biophysica Acta}}, journal = {BBA - Biomembranes}, year = {2013}, volume = {1828}, number = {11}, pages = {2592--2608}, month = nov } @article{Glomm:2011dp, author = {Glomm, Wilhelm R and Volden, Sondre and Ese, Marit-Helen Glomm and Halskau Jr., {\O}yvind}, title = {{Interactions of $\alpha$-Lactalbumin and Cytochrome cwith Langmuir Monolayers of Glycerophospholipids}}, journal = {Journal of Dispersion Science and Technology}, year = {2011}, volume = {32}, number = {2}, pages = {150--158}, month = jan } @article{Hanel:vn, author = {Hanel, Rudolf and Thurner, Stefan and Gell-Mann, Murray}, title = {{How multiplicity determines entropy and the derivation of the maximum entropy principle for complex systems}}, journal = {pnas.org} } @article{Shakhnovich:2006io, author = {Shakhnovich, Boris E and Koonin, Eugene V}, title = {{Origins and impact of constraints in evolution of gene families}}, journal = {Genome Res}, year = {2006}, volume = {16}, number = {12}, pages = {1529--1536} } @article{Kohavi:1995wf, author = {Kohavi, R}, title = {{A study of cross-validation and bootstrap for accuracy estimation and model selection}}, journal = {Ijcai}, year = {1995} } @article{Humphrey:1996bk, author = {Humphrey, William and Dalke, Andrew and Schulten, Klaus}, title = {{VMD: Visual molecular dynamics}}, journal = {Journal of Molecular Graphics}, year = {1996}, volume = {14}, number = {1}, pages = {33--38}, month = feb } @article{Lapinaite:2013gq, author = {Lapinaite, Audrone and Simon, Bernd and Skjaerven, Lars and Rakwalska-Bange, Magdalena and Gabel, Frank and Carlomagno, Teresa}, title = {{The structure of the box C/D enzyme reveals regulation of RNA methylation}}, journal = {Nature}, year = {2013}, volume = {502}, number = {7472}, pages = {519--523}, month = oct } @article{Pang:2005bg, author = {Pang, Andrew and Arinaminpathy, Yalini and Sansom, Mark S P and Biggin, Phillip C.}, title = {{Comparative molecular dynamics - Similar folds and similar motions?}}, journal = {Proteins: Struct., Funct., Bioinf.}, year = {2005}, volume = {61}, number = {4}, pages = {809--822} } @article{TAO:2009tx, author = {Tao, Terence}, title = {{STRUCTURE AND RANDOMNESS IN THE PRIME NUMBERS}}, year = {2009}, pages = {1--7}, month = sep } @phdthesis{Mohar:tt, author = {Mohar, Bojan}, title = {{THE LAPLACIAN SPECTRUM OF GRAPHS}}, school = {fmf.uni-lj.si} } @article{Foster:1997tt, author = {Foster, Provost and Tom, Fawcett}, title = {{Analysis and Visualization of Classifier Performance: Comparison under Imprecise Class and Cost Distributions}}, journal = {IN PROCEEDINGS OF THE THIRD INTERNATIONAL CONFERENCE ON KNOWLEDGE DISCOVERY AND DATA MINING}, year = {1997}, pages = {43--48} } @article{Jackson:2009ic, author = {Jackson, C J and Foo, J-L and Tokuriki, N and Afriat, L and Carr, P D and Kim, H-K and Schenk, G and Tawfik, D S and Ollis, D L}, title = {{Conformational sampling, catalysis, and evolution of the bacterial phosphotriesterase}}, journal = {Proc. Natl. Acad. Sci. U. S. A.}, year = {2009}, volume = {106}, number = {51}, pages = {21631--21636}, month = dec } @article{Hinsen:2010tk, author = {Hinsen, Konrad}, title = {{A Physicist{\textquoteright}s Guide to Crystallographic Data}}, year = {2010}, pages = {1--14}, month = jan } @article{Oldfield:2006ud, author = {Oldfield, C J and Su, E W and Uversky, V N and Dunker, A K}, title = {{Intrinsic Disorder in Transcription Factors{\dag} - Biochemistry (ACS Publications)}}, journal = {Biochemistry}, year = {2006} } @article{VanWijk:4HxWarh2, author = {Van Wijk, Jarke J.}, title = {{Unfolding the Earth: Myriahedral Projections}}, journal = {The Cartographic Journal}, year = {2007}, volume = {45}, number = {1}, pages = {32--34}, month = jan } @article{Anonymous:SnxG2oom, title = {{hungarian}}, year = {2004}, pages = {8} } @article{Marianayagam:2005ck, author = {Marianayagam, Neelan J and Jackson, Sophie E}, title = {{Native-state dynamics of the ubiquitin family: implications for function and evolution}}, journal = {Journal of the Royal Society, Interface / the Royal Society}, year = {2005}, volume = {2}, number = {2}, pages = {47--54}, month = mar } @article{Pontiggia:2007kn, author = {Pontiggia, F and Colombo, G. and Micheletti, C and Orland, H.}, title = {{Anharmonicity and self-similarity of the free energy landscape of protein G.}}, journal = {Phys. Rev. Lett.}, year = {2007}, volume = {98}, number = {4}, pages = {048102--048102}, month = jan } @article{Brust:2013gp, author = {Brust, Richard and Lukacs, Andras and Haigney, Allison and Addison, Kiri and Gil, Agnieszka and Towrie, Michael and Clark, Ian P and Greetham, Gregory M and Tonge, Peter J and Meech, Stephen R}, title = {{Proteins in Action: Femtosecond to Millisecond Structural Dynamics of a Photoactive Flavoprotein}}, journal = {JACS}, year = {2013}, volume = {135}, number = {43}, pages = {16168--16174}, month = oct } @article{Shanahan:2004hh, author = {Shanahan, H P and Thornton, J M}, title = {{An examination of the conservation of surface patch polarity for proteins}}, journal = {Bioinformatics}, year = {2004}, volume = {20}, number = {14}, pages = {2197--2204}, month = sep } @article{Chen:2004kk, author = {Chen, S-C}, title = {{Mining frequent patterns in protein structures: a study of protease families}}, journal = {Bioinformatics}, year = {2004}, volume = {20}, number = {suppl_1}, pages = {i77--i85}, month = aug } @article{Pal:2006iy, author = {P{\'a}l, Csaba and Papp, Bal{\'a}zs and Lercher, Martin J}, title = {{An integrated view of protein evolution}}, journal = {Nat Rev Genet}, year = {2006}, volume = {7}, number = {5}, pages = {337--348}, month = may } @article{Petre:2014uq, author = {Petre, Marian and Wilson, Greg}, title = {{Code Review For and By Scientists}}, year = {2014}, month = jul } @article{Perbet:2009wa, author = {Perbet, F and Stenger, B and Maki, A}, title = {{Random Forest Clustering and Application to Video Segmentation.}}, journal = {BMVC}, year = {2009} } @article{Elber:2010tv, author = {Elber, R}, title = {{Watching Biomolecular Machines in Action}}, journal = {Structure}, year = {2010} } @webpage{Anonymous:Cv63NEHI, author = {Goldstein, Harvey and Healy, Michael J. R.}, title = {{The Graphical Presentation of a Collection of Means}}, url = {http://www.jstor.org/stable/2983411} } @article{Zheng:2006fj, author = {Zheng, W and Brooks, B R and Thirumalai, D}, title = {{Low-frequency normal modes that describe allosteric transitions in biological nanomachines are robust to sequence variations}}, journal = {Proc. Natl. Acad. Sci. U. S. A.}, year = {2006}, volume = {103}, number = {20}, pages = {7664--7669}, month = may } @article{Kneller:2012bx, author = {Kneller, Gerald R and Hinsen, Konrad and Calligari, Paolo}, title = {{Communication: A minimal model for the diffusion-relaxation backbone dynamics of proteins}}, journal = {J. Chem. Phys.}, year = {2012}, volume = {136}, number = {19}, pages = {191101} } @article{Zhi:2010ih, author = {Zhi, Degui and Shatsky, Maxim and Brenner, Steven}, title = {{Alignment-free local structural search by writhe decomposition}}, journal = {Bioinformatics}, year = {2010}, volume = {26}, number = {9}, pages = {1176}, month = may } @article{Lovera:2012ig, author = {Lovera, Silvia and Sutto, Ludovico and Boubeva, Ralitza and Scapozza, Leonardo and D{\"o}lker, Nicole and Gervasio, Francesco L}, title = {{The Different Flexibility of c-Src and c-Abl Kinases Regulates the Accessibility of a Druggable Inactive Conformation}}, journal = {JACS}, year = {2012}, volume = {134}, number = {5}, pages = {2496--2499}, month = feb } @article{Vanwynsberghe:2006eu, author = {Van Wynsberghe, Adam W and Cui, Qiang}, title = {{Interpreting Correlated Motions Using Normal Mode Analysis}}, journal = {Structure}, year = {2006}, volume = {14}, number = {11}, pages = {1647--1653}, month = nov } @article{Anscombe:mDIyKxM0, author = {Anscombe, Francis J}, title = {{Frederick Mosteller and John W. Tukey: A Conversation}} } @inproceedings{Chazal:2011td, author = {Chazal, F and Guibas, L J and Oudot, S Y and Skraba, P}, title = {{Persistence-based clustering in riemannian manifolds}}, booktitle = {Proceedings of the 27th {\ldots}}, year = {2011} } @article{Bennett:2011kj, author = {Bennett, W F Drew and Tieleman, D Peter}, title = {{Water Defect and Pore Formation in Atomistic and Coarse-Grained Lipid Membranes: Pushing the Limits of Coarse Graining}}, journal = {J Chem Theory Comput}, year = {2011}, volume = {7}, number = {9}, pages = {2981--2988}, month = sep } @article{Ciriello:2008bq, author = {Ciriello, G and Guerra, C}, title = {{A review on models and algorithms for motif discovery in protein-protein interaction networks}}, journal = {Briefings in Functional Genomics and Proteomics}, year = {2008}, volume = {7}, number = {2}, pages = {147--156}, month = feb } @article{Kolodny:2005de, author = {Kolodny, R and Koehl, P and Levitt, M}, title = {{Comprehensive evaluation of protein structure alignment methods: Scoring by geometric measures}}, journal = {J. Mol. Biol.}, year = {2005}, volume = {346}, number = {4}, pages = {1173--1188} } @article{Canaan:2002dp, author = {Canaan, St{\'e}phane and Nielsen, Robert and Ghomashchi, Farideh and Robinson, Bruce H and Gelb, Michael H}, title = {{Unusual mode of binding of human group IIA secreted phospholipase A2 to anionic interfaces as studied by continuous wave and time domain electron paramagnetic resonance spectroscopy.}}, journal = {J. Biol. Chem.}, year = {2002}, volume = {277}, number = {34}, pages = {30984--30990}, month = aug } @article{Sugita:2008vs, author = {Sugita, Y and Mitsutake, A and Okamoto, Y}, title = {{Generalized-Ensemble Algorithms for Protein Folding Simulations}}, journal = {Rugged Free Energy Landscapes}, year = {2008}, pages = {369--407} } @article{Anonymous:ZL4ImefJ, title = {{A Scientist's Nightmare: Software Problem Leads to Five Retractions}} } @webpage{B:5bg8pDyo, author = {B, Efron}, title = {{The Jacknife, the bootstrap, and other resampling plans}}, url = {https://statistics.stanford.edu/sites/default/files/EFS%20NSF%20163.pdf} } @article{Fernandez:2011ia, author = {Fern{\'a}ndez, Jose D and Vico, Francisco J}, title = {{Automating the search of molecular motor templates by evolutionary methods}}, journal = {Biosystems}, year = {2011}, volume = {106}, number = {2-3}, pages = {82--93}, month = nov } @article{Soare:2008uz, author = {Soare, RI}, title = {{Computability and Recursion}}, year = {2008}, pages = {1--46}, month = jun } @article{Gekko:1979bo, author = {Gekko, Kunihiko and Noguchi, Hajime}, title = {{Compressibility of globular proteins in water at 25.degree.C}}, journal = {J. Phys. Chem.}, year = {1979}, volume = {83}, number = {21}, pages = {2706--2714}, month = oct } @article{Miller:1987un, author = {Miller, Susan and Janin, Jo{\"e}l and Lesk, Arthur M. and Chothia, Cyrus}, title = {{Interior and surface of monomeric proteins.}}, journal = {J. Mol. Biol.}, year = {1987}, volume = {196}, number = {3}, pages = {641--656}, month = aug } @article{Arcario:2014ij, author = {Arcario, Mark J and Tajkhorshid, Emad}, title = {{Membrane-Induced Structural Rearrangement and Identification of a Novel Membrane Anchor in Talin F2F3}}, journal = {Biophys. J.}, year = {2014}, volume = {107}, number = {9}, pages = {2059--2069}, month = nov } @article{Fukunaga:1989ix, author = {Fukunaga, K and Hayes, R R}, title = {{Effects of sample size in classifier design}}, journal = {IEEE Trans. Pattern Anal. Machine Intell.}, year = {1989}, volume = {11}, number = {8}, pages = {873--885} } @article{Gilson:1997iz, author = {Gilson, M K and Given, J A and Bush, B L and McCammon, J A}, title = {{The statistical-thermodynamic basis for computation of binding affinities: a critical review}}, journal = {Biophys. J.}, year = {1997}, volume = {72}, number = {3}, pages = {1047--1069}, month = mar } @article{Baldini:2005eq, author = {Baldini, G and Cannone, F and Chirico, G}, title = {{Pre-unfolding resonant oscillations of single green fluorescent protein molecules}}, journal = {Science}, year = {2005}, volume = {309}, number = {5737}, pages = {1096--1100} } @article{Kurkcuoglu:2016cb, author = {Kurkcuoglu, Zeynep and Bahar, Ivet and Doruker, Pemra}, title = {{ClustENM: ENM-Based Sampling of Essential Conformational Space at Full Atomic Resolution}}, journal = {J Chem Theory Comput}, year = {2016}, volume = {12}, number = {9}, pages = {4549--4562}, month = sep } @article{Yang:1996vu, author = {Yang, Fan and Phillips, George N. Jr}, title = {{Crystal structures of CO-, deoxy- and met-myoglobins at various pH values}}, journal = {J. Mol. Biol.}, year = {1996}, volume = {256}, number = {4}, pages = {762--774} } @article{Atilgan:2012vr, author = {Atilgan, C and Okan, O B and Atilgan, A R}, title = {{Network-Based Models as Tools Hinting at Nonevident Protein Functionality - Annual Review of Biophysics, 41(1):205}}, journal = {Annu. Rev. Biophys.}, year = {2012} } @article{Huang:2014gp, author = {Huang, Tsun-Tsao and del Valle Marcos, Mar{\'\i}a Laura and Hwang, Jenn-Kang and Echave, Juli{\'a}n}, title = {{A mechanistic stress model of protein evolution accounts for site-specific evolutionary rates and their relationship with packing density and flexibility}}, journal = {BMC Evol Biol}, year = {2014}, volume = {14}, number = {1}, pages = {78} } @article{Ohta:1992wp, author = {Ohta, T}, title = {{The nearly neutral theory of molecular evolution}}, journal = {Annual Review of Ecology and Systematics}, year = {1992}, volume = {23}, number = {1}, pages = {263--286} } @article{Coombes:2007iu, author = {Coombes, Kevin R and Wang, Jing and Baggerly, Keith A}, title = {{Microarrays: retracing steps}}, journal = {Nature Medicine}, year = {2007}, volume = {13}, number = {11}, pages = {1276}, month = nov } @article{Evans:2015tv, author = {Evans, R and Wilding, N B}, title = {{Quantifying density fluctuations in water at a hydrophobic surface: evidence for critical drying}}, journal = {Phys. Rev. Lett.}, year = {2015}, eprint = {related:SN4_9ovtnpgJ}, eprinttype = {scholar} } @article{Alexander:1998ib, author = {Alexander, Shlomo}, title = {{Amorphous solids: their structure, lattice dynamics and elasticity}}, journal = {Physics Reports}, year = {1998}, volume = {296}, number = {2-4}, pages = {65--236}, month = mar } @article{Bahar:2007jj, author = {Bahar, Ivet and Chennubhotla, Chakra and Erman, Burak}, title = {{Reply to `Comment on elastic network models and proteins'}}, journal = {Phys. Biol.}, year = {2007}, volume = {4}, number = {1}, pages = {64--65} } @article{Balsera:1996wp, author = {Balsera, MA and Wriggers, W and Oono, Y and Schulten, K}, title = {{Principal component analysis and long time protein dynamics}}, journal = {J Phys Chem-Us}, year = {1996}, volume = {100}, number = {7}, pages = {2567--2572} } @article{Shurki:2004wl, author = {Shurki, A and Warshel, A}, title = {{Why does the Ras switch {\textquotedblleft}break{\textquotedblright} by oncogenic mutations?}}, journal = {Proteins: Struct., Funct., Bioinf.}, year = {2004}, volume = {55}, number = {1}, pages = {1--10} } @article{Williams:1996ed, author = {Williams, Roger L and Katan, Matilda}, title = {{Structural views of phosphoinositide-specific phospholipase C: signalling the way ahead}}, journal = {Structure}, year = {1996}, volume = {4}, number = {12}, pages = {1387--1394}, month = dec } @article{Sigal:1994wx, author = {Sigal, C T and Zhou, W and Buser, C A and McLaughlin, S and Resh, M D}, title = {{Amino-terminal basic residues of Src mediate membrane binding through electrostatic interaction with acidic phospholipids}}, journal = {Proceedings of the {\ldots}}, year = {1994} } @article{BOOTH:1994bq, author = {BOOTH, J G and BUTLER, R W and HALL, P}, title = {{Bootstrap Methods for Finite Populations}}, journal = {Journal of the American Statistical Association}, year = {1994}, volume = {89}, number = {428}, pages = {1282--1289}, month = dec } @article{Derpanis:2009uy, author = {Derpanis, Konstantinos G}, title = {{The Bhattacharyya Measure}}, year = {2009}, pages = {1--3}, month = jan } @article{Anonymous:vr2dt-Sw, title = {{ess}}, year = {2007}, pages = {3} } @article{Lange:2005gv, author = {Lange, Oliver F and Grubm{\"u}ller, Helmut}, title = {{Generalized correlation for biomolecular dynamics}}, journal = {Proteins: Struct., Funct., Bioinf.}, year = {2005}, volume = {62}, number = {4}, pages = {1053--1061}, month = dec } @article{HOLM:1998uq, author = {HOLM, L and SANDER, C}, title = {{Dictionary of recurrent domains in protein structures}}, year = {1998}, volume = {33}, number = {1}, pages = {88--96} } @article{Pennington:2011fe, author = {Pennington, M and Helle, K}, title = {{Evaluation of the design and efficiency of the Norwegian self-sampling purse-seine reference fleet}}, journal = {ICES J. Mar. Sci.}, year = {2011}, volume = {68}, number = {8}, pages = {1764--1768}, month = aug } @article{HOPKINS:1991gk, author = {HOPKINS, C C E and NILSSEN, E M}, title = {{The rise and fall of the Barents Sea capelin (Mallotus villosus): a multivariate scenario}}, journal = {Polar Research}, year = {1991}, volume = {10}, number = {2}, pages = {535--546}, month = dec } @inproceedings{Drummond:66nGJCmx, author = {Drummond, Chris}, title = {{Replicability is not Reproducibility: Nor is it Good Science}}, booktitle = {cogprints.org} } @article{PaulCharlesWhitford:2008jx, author = {Paul Charles Whitford, Jos{\'e} Nelson Onuchic Peter Guy Wolynes}, title = {{Energy landscape along an enzymatic reaction trajectory: hinges or cracks?}}, journal = {HFSP Journal}, year = {2008}, volume = {2}, number = {2}, pages = {61}, month = apr } @article{MacCallum:2007iq, author = {MacCallum, J L and Bennett, W F D and Tieleman, D P}, title = {{Partitioning of Amino Acid Side Chains into Lipid Bilayers: Results from Computer Simulations and Comparison to Experiment}}, journal = {The Journal of General Physiology}, year = {2007}, volume = {129}, number = {5}, pages = {371--377}, month = apr } @article{Velankar:2009he, author = {Velankar, S and Best, C and Beuth, B and Boutselakis, C H and Cobley, N and Sousa Da Silva, A W and Dimitropoulos, D and Golovin, A and Hirshberg, M and John, M and Krissinel, E B and Newman, R and Oldfield, T and Pajon, A and Penkett, C J and Pineda-Castillo, J and Sahni, G and Sen, S and Slowley, R and Suarez-Uruena, A and Swaminathan, J and van Ginkel, G and Vranken, W F and Henrick, K and Kleywegt, G J}, title = {{PDBe: Protein Data Bank in Europe}}, journal = {Nucleic Acids Res.}, year = {2009}, volume = {38}, number = {Database}, pages = {D308--D317}, month = dec } @article{Mamonova:2013hz, author = {Mamonova, Tatyana B and Glyakina, Anna V and Galzitskaya, Oxana V and Kurnikova, Maria G}, title = {{Stability and rigidity/flexibility{\textemdash}Two sides of the same coin?}}, journal = {Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics}, year = {2013}, volume = {1834}, number = {5}, pages = {854--866}, month = may } @webpage{Anonymous:aAMVEkjN, title = {{552.full.pdf}}, url = {http://vir.sgmjournals.org/content/92/3/552.full.pdf} } @article{Hinz:2012ik, author = {Hinz, H and Murray, L G and Lambert, G I and Hiddink, J G and Kaiser, M J}, title = {{Confidentiality over fishing effort data threatens science and management progress}}, journal = {Fish Fish}, year = {2012}, pages = {n/a--n/a}, month = may } @article{Shen:1997vo, author = {Shen, L and Bassolino, D and Stouch, T}, title = {{Transmembrane helix structure, dynamics, and interactions: multi-nanosecond molecular dynamics simulations}}, journal = {Biophys. J.}, year = {1997}, volume = {73}, number = {1}, pages = {3--20} } @article{Jorde:2004tt, author = {Jorde, LB and Wooding, SP}, title = {{Genetic variation, classification and'race'}}, journal = {Nature Genetics}, year = {2004}, volume = {36}, pages = {S28--S33} } @article{Hou:2005us, author = {Hou, J and Jun, SR and Zhang, C and Kim, SH}, title = {{Global mapping of the protein structure space and application in structure-based inference of protein function}}, journal = {Proc. Natl. Acad. Sci. U. S. A.}, year = {2005}, volume = {102}, number = {10}, pages = {3651} } @article{DosSantos:2013iz, author = {Dos Santos, Helena G and Klett, Javier and M{\'e}ndez, Raul and Bastolla, Ugo}, title = {{Characterizing conformation changes in proteins through the torsional elastic response}}, journal = {Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics}, year = {2013}, volume = {1834}, number = {5}, pages = {836--846}, month = may } @article{Anonymous:TscZx4Cz, title = {{M7CL Owner's Manual}}, year = {2007}, pages = {1--282}, month = dec } @article{Schuyler:2009ij, author = {Schuyler, Adam D and Jernigan, Robert L and Qasba, Pradman K and Ramakrishnan, Boopathy and Chirikjian, Gregory S}, title = {{Iterative cluster-NMA: A tool for generating conformational transitions in proteins}}, journal = {Proteins: Struct., Funct., Bioinf.}, year = {2009}, volume = {74}, number = {3}, pages = {760--776}, month = feb } @article{Devaux:2004ic, author = {Devaux, Philippe F and Morris, Roger}, title = {{Transmembrane Asymmetry and Lateral Domains in Biological Membranes}}, journal = {Traffic}, year = {2004}, volume = {5}, number = {4}, pages = {241--246}, month = mar } @article{Livesay:2008hi, author = {Livesay, Dennis R and Huynh, Dang H and Dallakyan, Sargis and Jacobs, Donald J}, title = {{Hydrogen bond networks determine emergent mechanical and thermodynamic properties across a protein family}}, journal = {Chemistry Central Journal}, year = {2008}, volume = {2}, number = {1}, pages = {17} } @article{Ariyaratne:2014jc, author = {Ariyaratne, Amila and Wu, Chenhao and Tseng, Chiao-Yu and Zocchi, Giovanni}, title = {{Dissipative Dynamics of Enzymes}}, journal = {Phys. Rev. Lett.}, year = {2014}, volume = {113}, number = {19}, pages = {198101}, month = nov } @article{Singh:2014gh, author = {Singh, Jogender and Kumar, Harish and Sabareesan, Ambadi T and Udgaonkar, Jayant B}, title = {{Rational Stabilization of Helix 2 of the Prion Protein Prevents Its Misfolding and Oligomerization}}, journal = {JACS}, year = {2014}, volume = {136}, number = {48}, pages = {16704--16707}, month = dec } @article{Arkin:1998ui, author = {Arkin, I T and Brunger, A T}, title = {{Statistical analysis of predicted transmembrane alpha-helices.}}, journal = {Biochim. Biophys. Acta}, year = {1998}, volume = {1429}, number = {1}, pages = {113--128}, month = dec } @article{Mailliard:1997db, author = {Mailliard, William S and Luecke, Hartmut and Haigler, Harry T}, title = {{Annexin XII Forms Calcium-Dependent Multimers in Solution and on Phospholipid Bilayers:~ A Chemical Cross-Linking Study {\dag}}}, journal = {Biochemistry}, year = {1997}, volume = {36}, number = {29}, pages = {9045--9050}, month = jul } @article{Rankin:2015di, author = {Rankin, Blake M and Ben-Amotz, Dor and van der Post, Sietse T and Bakker, Huib J}, title = {{Contacts Between Alcohols in Water Are Random Rather than Hydrophobic}}, journal = {J. Phys. Chem. Lett.}, year = {2015}, volume = {6}, number = {4}, pages = {688--692}, month = feb } @article{Cho:2005bq, author = {Cho, Wonhwa and Stahelin, Robert V}, title = {{Membrane-Protein Interactions in Cell Signaling and Membrane Trafficking}}, journal = {Annu Rev Bioph Biom}, year = {2005}, volume = {34}, number = {1}, pages = {119--151}, month = jun } @article{Wolf:1999vo, author = {Wolf, YI and Aravind, L and Grishin, NV and Koonin, EV}, title = {{Evolution of aminoacyl-tRNA synthetases - Analysis of unique domain architectures and phylogenetic trees reveals a complex history of horizontal gene transfer events}}, journal = {Genome Res}, year = {1999}, volume = {9}, number = {8}, pages = {689--710} } @article{LENZ:1951ux, author = {LENZ, F}, title = {{THE RATIO OF PROTON AND ELECTRON MASSES}}, journal = {Phys Rev}, year = {1951}, volume = {82}, number = {4}, pages = {554--554} } @article{Kabsch:1983bp, author = {Kabsch, W and SANDER, C}, title = {{Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features.}}, journal = {Biopolymers}, year = {1983}, volume = {22}, number = {12}, pages = {2577--2637}, month = dec } @article{GERSTEIN:1994vy, author = {GERSTEIN, M and LESK, AM and Chothia, Cyrus}, title = {{STRUCTURAL MECHANISMS FOR DOMAIN MOVEMENTS IN PROTEINS}}, journal = {Biochemistry}, year = {1994}, volume = {33}, number = {22}, pages = {6739--6749} } @article{Dror:2003bd, author = {Dror, O and Benyamini, H and Nussinov, R and Wolfson, HJ}, title = {{Multiple structural alignment by secondary structures: Algorithm and applications}}, journal = {Protein Sci.}, year = {2003}, volume = {12}, number = {11}, pages = {2492--2507} } @article{Scott:1990wf, author = {Scott, D L and White, S P and Otwinowski, Z and Yuan, W and Gelb, M H and Sigler, P B}, title = {{Interfacial catalysis: the mechanism of phospholipase A2.}}, journal = {Science}, year = {1990}, volume = {250}, number = {4987}, pages = {1541--1546}, month = dec } @article{Zheng:2005gs, author = {Zheng, WJ and Brooks, BR and Doniach, S and Thirumalai, D}, title = {{Network of dynamically important residues in the open/closed transition in polymerases is strongly conserved}}, journal = {Structure}, year = {2005}, volume = {13}, number = {4}, pages = {565--577} } @article{Devaux:1991hl, author = {Devaux, Philippe F}, title = {{Static and dynamic lipid asymmetry in cell membranes}}, journal = {Biochemistry}, year = {1991}, volume = {30}, number = {5}, pages = {1163--1173}, month = feb } @article{Siglioccolo:2010if, author = {Siglioccolo, Alessandro and Gerace, Raffaele and Pascarella, Stefano}, title = {{{\textquotedblleft}Cold spots{\textquotedblright} in protein cold adaptation: Insights from normalized atomic displacement parameters (B{\textasciiacute}-factors)}}, journal = {Biophys. Chem.}, year = {2010}, volume = {153}, number = {1}, pages = {104--114}, month = dec } @article{Juritz:2012gw, author = {Juritz, E and Palopoli, N and Fornasari, M S and Fernandez-Alberti, S and Parisi, G}, title = {{Protein Conformational Diversity Modulates Sequence Divergence}}, journal = {Molecular Biology and Evolution}, year = {2012}, volume = {30}, number = {1}, pages = {79--87}, month = dec } @article{Steele:1985hu, author = {Steele, John H}, title = {{A comparison of terrestrial and marine ecological systems}}, journal = {Nature}, year = {1985}, volume = {313}, number = {6001}, pages = {355--358}, month = jan } @article{Krivov:2010vk, author = {Krivov, SV}, title = {{Is Protein Folding Sub-Diffusive?}}, journal = {PLoS Comput. Biol.}, year = {2010}, volume = {6}, number = {9}, pages = {868--893} } @article{Lazaridis:1999up, author = {Lazaridis, T and Karplus, M}, title = {{Effective energy function for proteins in solution - Lazaridis - 1999 - Proteins: Structure, Function, and Bioinformatics - Wiley Online Library}}, journal = {Proteins: Structure}, year = {1999} } @webpage{Anonymous:oObD9DJ0, title = {{PLOS Computational Biology: The LUX Score: A Metric for Lipidome Homology}}, url = {http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004511} } @article{Kolodny:2006jv, author = {Kolodny, Rachel and Petrey, Donald and Honig, Barry}, title = {{Protein structure comparison: implications for the nature of 'fold space', and structure and function prediction}}, journal = {Current Opinion in Structural Biology}, year = {2006}, volume = {16}, number = {3}, pages = {393--398} } @article{Stahelin:2008fh, author = {Stahelin, R V}, title = {{Lipid binding domains: more than simple lipid effectors}}, journal = {The Journal of Lipid Research}, year = {2008}, volume = {50}, number = {Supplement}, pages = {S299--S304}, month = dec } @webpage{Anonymous:g6EVmRAV, title = {{Interactions between misfolded protein oligomers and membranes: A central topic in neurodegenerative diseases?}}, url = {http://www.sciencedirect.com/science/article/pii/S0005273615000280} } @article{Anonymous:SnxG2oom, title = {{hungarian}}, year = {2004}, pages = {8} } @webpage{Anonymous:HLcseC02, title = {{The Winnower | Verifiable research: The missing link between replicability and reproducibility}}, url = {https://thewinnower.com/papers/4770-verifiable-research-the-missing-link-between-replicability-and-reproducibility} } @article{Carnevale:2007vs, author = {Carnevale, V and Raugei, S and Micheletti, C and Carloni, P}, title = {{Large-Scale Motions and Electrostatic Properties of Furin and HIV-1 Protease{\dag}}}, journal = {J Phys Chem A}, year = {2007}, volume = {111}, number = {49}, pages = {12327--12332} } @article{CarterJr:2015if, author = {Carter Jr., Charles W and Wolfenden, Richard}, title = {{tRNA acceptor stem and anticodon bases form independent codes related to protein folding}}, journal = {Proc. Natl. Acad. Sci. U. S. A.}, year = {2015}, volume = {112}, number = {24}, pages = {7489--7494}, month = jun } @article{Skowronek:2004jj, author = {Skowronek, Karlheinz R and Guo, Fukun and Zheng, Yi and Nassar, Nicolas}, title = {{The C-terminal basic tail of RhoG assists the guanine nucleotide exchange factor Trio in binding to phospholipids}}, journal = {J. Biol. Chem.}, year = {2004}, volume = {279}, number = {36}, pages = {37895--37907}, month = sep } @article{Saelensminde:2010vz, author = {S{\ae}lensminde, Gisle and Reuter, Nathalie and Jonassen, Inge}, title = {{allostery_preprint}}, year = {2010}, pages = {1--25}, month = jan } @article{Gabdoulline:1996ue, author = {Gabdoulline, RR and Wade, RC}, title = {{Effective charges for macromolecules in solvent}}, journal = {J Phys Chem-Us}, year = {1996}, volume = {100}, number = {9}, pages = {3868--3878} } @article{Iversen:2002fja, author = {Iversen, H and Fuglebakk, E and Holmsen, H and Fukami, MH}, title = {{Identification of minor metabolites of phospholipid signal molecules in [P-32]P-i-labelled platelets}}, journal = {Platelets}, year = {2002}, volume = {13}, number = {5-6}, pages = {279--284} } @article{Munz:2010iza, author = {M{\"u}nz, M{\'a}rton and Lyngs{\o}, Rune and Hein, Jotun and Biggin, Philip}, title = {{Additional file: Dynamics based alignment of proteins: an alternative approach to quantify dynamic similarity}}, journal = {BMC Bioinformatics}, year = {2010}, volume = {11}, number = {1}, pages = {188}, month = apr } @article{Hamre:1994hd, author = {Hamre, Johannes}, title = {{Biodiversity and exploitation of the main fish stocks in the Norwegian - Barents Sea ecosystem}}, journal = {Biodivers Conserv}, year = {1994}, volume = {3}, number = {6}, pages = {473--492} } @article{Taylor:2000fq, author = {Taylor, William R}, title = {{A deeply knotted protein structure and how it might fold}}, journal = {Nature}, year = {2000}, volume = {406}, number = {6798}, pages = {916--919}, month = aug } @article{Bahar:2007jj, author = {Bahar, Ivet and Chennubhotla, Chakra and Erman, Burak}, title = {{Reply to {\textquoteleft}Comment on elastic network models and proteins{\textquoteright}}}, journal = {Phys. Biol.}, year = {2007}, volume = {4}, number = {1}, pages = {64--65}, month = apr } @article{Calandrini:2008fn, author = {Calandrini, Vania and Abergel, Daniel and Kneller, Gerald R}, title = {{Protein dynamics from a NMR perspective: Networks of coupled rotators and fractional Brownian dynamics}}, journal = {J. Chem. Phys.}, year = {2008}, volume = {128}, number = {14}, pages = {145102--145102--8} } @article{Jonsson:2013wl, author = {J{\'o}nsson, S {\AE} and Mitternacht, S and Irb{\"a}ck, A}, title = {{Mechanical resistance in unstructured proteins}}, year = {2013}, month = apr } @article{MacKerell:1998jn, author = {MacKerell, A D and Bashford, D and Bellott and Dunbrack, R L and Evanseck, J D and Field, M J and Fischer, S and Gao, J and Guo, H and Ha, S and Joseph-McCarthy, D and Kuchnir, L and Kuczera, K and Lau, F T K and Mattos, C and Michnick, S and Ngo, T and Nguyen, D T and Prodhom, B and Reiher, W E and Roux, B and Schlenkrich, M and Smith, J C and Stote, R and Straub, J and Watanabe, M and Wi{\'o}rkiewicz-Kuczera, J and Yin, D and Karplus, M}, title = {{All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins {\dag}}}, journal = {J. Phys. Chem. B}, year = {1998}, volume = {102}, number = {18}, pages = {3586--3616}, month = apr } @article{Baldwin:1986ul, author = {Baldwin, R L}, title = {{Temperature dependence of the hydrophobic interaction in protein folding}}, journal = {Proceedings of the National Academy of {\ldots}}, year = {1986} } @article{Echave:2010es, author = {Echave, Juli{\'a}n and Fern{\'a}ndez, Francisco M}, title = {{A perturbative view of protein structural variation}}, journal = {Proteins: Struct., Funct., Bioinf.}, year = {2010}, volume = {78}, number = {1}, pages = {173--180} } @article{Hess:2008db, author = {Hess, Berk and Kutzner, Carsten and van der Spoel, David and Lindahl, Erik}, title = {{GROMACS 4:~ Algorithms for highly efficient, load-balanced, and scalable molecular simulation}}, journal = {J Chem Theory Comput}, year = {2008}, volume = {4}, number = {3}, pages = {435--447}, month = mar } @article{Schrank:2009gf, author = {Schrank, Travis P and Bolen, D Wayne and Hilser, Vincent J}, title = {{Rational modulation of conformational fluctuations in adenylate kinase reveals a local unfolding mechanism for allostery and functional adaptation in proteins.}}, journal = {Proc. Natl. Acad. Sci. U. S. A.}, year = {2009}, volume = {106}, number = {40}, pages = {16984--16989}, month = oct } @article{Reisser:2014jc, author = {Rei{\ss}er, Sabine and Strandberg, Erik and Steinbrecher, Thomas and Ulrich, Anne S}, title = {{3D Hydrophobic Moment Vectors as a Tool to Characterize the Surface Polarity of Amphiphilic Peptides}}, journal = {Biophys. J.}, year = {2014}, volume = {106}, number = {11}, pages = {2385--2394}, month = jun } @article{Anonymous:xynuDwyO, title = {{Matching}}, year = {2003}, pages = {6}, month = dec } @article{Illergard:2010ep, author = {Illergard, Kristoffer and Kauko, Anni and Elofsson, Arne}, title = {{Why are polar residues within the membrane core evolutionary conserved?}}, journal = {Proteins: Struct., Funct., Bioinf.}, year = {2010}, volume = {79}, number = {1}, pages = {79--91}, month = oct } @article{Micheletti:1998wj, author = {Micheletti, C and Banavar, JR and Maritan, A and Seno, F}, title = {{Steric constraints in model proteins}}, journal = {Phys. Rev. Lett.}, year = {1998}, volume = {80}, number = {25}, pages = {5683--5686} } @article{Lin:2008cr, author = {Lin, Chih-Peng and Huang, Shao-Wei and Lai, Yan-Long and Yen, Shih-Chung and Shih, Chien-Hua and Lu, Chih-Hao and Huang, Cuen-Chao and Hwang, Jenn-Kang}, title = {{Deriving protein dynamical properties from weighted protein contact number}}, journal = {Proteins: Struct., Funct., Bioinf.}, year = {2008}, volume = {72}, number = {3}, pages = {929--935}, month = feb } @article{Nilsson:2005iq, author = {Nilsson, Johan and Persson, Bengt and von Heijne, Gunnar}, title = {{Comparative analysis of amino acid distributions in integral membrane proteins from 107 genomes}}, journal = {Proteins: Struct., Funct., Bioinf.}, year = {2005}, volume = {60}, number = {4}, pages = {606--616}, month = jul } @article{Hinsen:2011ti, author = {Hinsen, Konrad}, title = {{Elastic network models}}, year = {2011}, pages = {1--21}, month = sep } @article{Douliez:1998dh, author = {Douliez, J P and Ferrarini, A and Dufourc, E J}, title = {{On the relationship between C-C and C-D order parameters and its use for studying the conformation of lipid acyl chains in biomembranes}}, journal = {J. Chem. Phys.}, year = {1998}, volume = {109}, number = {6}, pages = {2513} } @article{Satopaa:2011ww, author = {Satopaa, Ville and Albrecht, Jeannie and Irwin, David and Raghavan, Barath}, title = {{Finding a "Kneedle" in a Haystack: Detecting Knee Points in System Behavior}}, year = {2011}, pages = {166--171} } @article{Cohen:1994bs, author = {Cohen, F and Pan, K and Huang, Z and Baldwin, M and Fletterick, R and Prusiner, S}, title = {{Structural clues to prion replication}}, journal = {Science}, year = {1994}, volume = {264}, number = {5158}, pages = {530--531}, month = apr } @article{Roosild:2005hc, author = {Roosild, T P}, title = {{NMR Structure of Mistic, a Membrane-Integrating Protein for Membrane Protein Expression}}, journal = {Science}, year = {2005}, volume = {307}, number = {5713}, pages = {1317--1321}, month = feb } @article{Anderson:2017ja, author = {Anderson, Sean C and Cooper, Andrew B and Jensen, Olaf P and Minto, C{\'o}il{\'\i}n and Thorson, James T and Walsh, Jessica C and Afflerbach, Jamie and Dickey-Collas, Mark and Kleisner, Kristin M and Longo, Catherine and Osio, Giacomo Chato and Ovando, Daniel and Mosqueira, Iago and Rosenberg, Andrew A and Selig, Elizabeth R}, title = {{Improving estimates of population status and trend with superensemble models}}, journal = {Fish Fish}, year = {2017}, volume = {24}, pages = {173--10}, month = jan } @article{Herzog:2016iu, author = {Herzog, Florian A and Braun, Lukas and Schoen, Ingmar and Vogel, Viola}, title = {{Improved Side Chain Dynamics in MARTINI Simulations of Protein{\textendash}Lipid Interfaces}}, journal = {J Chem Theory Comput}, year = {2016}, pages = {acs.jctc.6b00122}, month = apr } @article{Spiwok:2007ec, author = {Spiwok, Vojtech and Lipovova, Petra and Skalova, Tereza and Duskova, Jarmila and Dohnalek, Jan and Hasek, Jindrich and Russell, Nicholas J and Kralova, Blanka}, title = {{Cold-active enzymes studied by comparative molecular dynamics simulation}}, journal = {J Mol Model}, year = {2007}, volume = {13}, number = {4}, pages = {485--497} } @article{Chng:2008tz, author = {Chng, C and Yang, L}, title = {{Coarse-Grained Models Reveal Functional Dynamics{\textendash}II. Molecular Dynamics Simulation at {\ldots}}}, journal = {Bioinformatics and Biology Insights}, year = {2008} } @article{Sampaio:2011wm, author = {Sampaio, Julio L and Gerl, Mathias J and Klose, Christian and Ejsing, Christer S and Beug, Hartmut and Simons, Kai and Shevchenko, Andrej}, title = {{Membrane lipidome of an epithelial cell line}}, journal = {Proceedings of the {\ldots}}, year = {2011} } @article{Krieg:2016cl, author = {Krieg, Sabine and Boonstra, Harm Jan and Smeets, Marc}, title = {{Small-Area Estimation with Zero-Inflated Data {\textendash} a Simulation Study}}, journal = {Journal of Official Statistics}, year = {2016}, volume = {32}, number = {4}, pages = {963--986}, month = dec } @article{Kondrashov:2006iu, author = {Kondrashov, Dmitry A and Cui, Qiang and Phillips, George N. Jr}, title = {{Optimization and evaluation of a coarse-grained model of protein motion using X-ray crystal data}}, journal = {Biophys. J.}, year = {2006}, volume = {91}, number = {8}, pages = {2760--2767}, month = oct } @article{SciPyOpenSourceS:g1eMLzGE, author = {Jones, E and Oliphant, E and Peterson, P}, title = {{SciPy: Open Source Scientific Tools for Python}} } @article{Riccardi:2009ic, author = {Riccardi, Demian and Cui, Qiang and Phillips, George N. Jr}, title = {{Application of Elastic Network Models to Proteins in the Crystalline State}}, journal = {Biophys. J.}, year = {2009}, volume = {96}, number = {2}, pages = {464--475} } @article{Echave:2008ki, author = {Echave, Juli{\'a}n}, title = {{Evolutionary divergence of protein structure: The linearly forced elastic network model}}, journal = {Chem. Phys. Lett.}, year = {2008}, volume = {457}, number = {4-6}, pages = {413--416}, month = may } @article{Anonymous:9C4CGRsq, title = {{User Guide Hamax Bicycle child seats}}, year = {2010}, pages = {1--15}, month = apr } @article{Huang:2008kt, author = {Huang, Xuhui and Bowman, Gregory R and Pande, Vijay S}, title = {{Convergence of folding free energy landscapes via application of enhanced sampling methods in a distributed computing environment}}, journal = {J. Chem. Phys.}, year = {2008}, volume = {128}, number = {20}, pages = {205106} } @article{GELB:1999ht, author = {GELB, M and Cho, W and WILTON, D}, title = {{Interfacial binding of secreted phospholipases A2: more than electrostatics and a major role for tryptophan}}, journal = {Current Opinion in Structural Biology}, year = {1999}, volume = {9}, number = {4}, pages = {428--432}, month = aug } @article{FRAUENFELDER:1991wi, author = {FRAUENFELDER, H and SLIGAR, SG and WOLYNES, PG}, title = {{The Energy Landscapes and Motions of Proteins}}, journal = {Science}, year = {1991}, volume = {254}, number = {5038}, pages = {1598--1603} } @article{Anonymous:-DHHWTqF, title = {{assignment}}, year = {2005}, pages = {6}, month = mar } @article{vanDijk:2016im, author = {van Dijk, Erik and Varilly, Patrick and Knowles, Tuomas P J and Frenkel, Daan and Abeln, Sanne}, title = {{Consistent Treatment of Hydrophobicity in Protein Lattice Models Accounts for Cold Denaturation}}, journal = {Phys. Rev. Lett.}, year = {2016}, volume = {116}, number = {7}, pages = {078101}, month = feb } @article{Morra:2012kl, author = {Morra, Giulia and Potestio, Raffaello and Micheletti, Cristian and Colombo, Giorgio}, title = {{Corresponding Functional Dynamics across the Hsp90 Chaperone Family: Insights from a Multiscale Analysis of MD Simulations}}, journal = {PLoS Comput. Biol.}, year = {2012}, volume = {8}, number = {3}, pages = {e1002433}, month = mar } @article{Lin:2014wt, author = {Lin, D and Grossfield, A}, title = {{Thermodynamics of Antimicrobial Lipopeptide Binding to Membranes: Origins of Affinity and Selectivity}}, journal = {Biophys. J.}, year = {2014} } @article{Victor:1999he, author = {Victor, Ken and Jacob, Jaison and Cafiso, David S}, title = {{Interactions Controlling the Membrane Binding of Basic Protein Domains:~ Phenylalanine and the Attachment of the Myristoylated Alanine-Rich C-Kinase Substrate Protein to Interfaces {\dag}}}, journal = {Biochemistry}, year = {1999}, volume = {38}, number = {39}, pages = {12527--12536}, month = sep } @article{Mueller:uq, author = {Mueller, Benjamin K and Subramaniam, Sabareesh and Senes, Alessandro}, title = {{A frequent, GxxxG-mediated, transmembrane association motif is optimized for the formation of interhelical C$\alpha${\textendash}H hydrogen bonds}}, journal = {pnas.org} } @article{Anderson:1963uc, author = {Anderson, T}, title = {{Asymptotic Theory for Principal Component Analysis}}, journal = {The Annals of Mathematical Statistics}, year = {1963}, volume = {34}, number = {1}, pages = {122--148}, month = mar } @article{Mattingly:2018jk, author = {Mattingly, Henry H and Transtrum, Mark K and Abbott, Michael C and Machta, Benjamin B}, title = {{Maximizing the information learned from finite data selects a simple model}}, journal = {Proc Natl Acad Sci U S A}, year = {2018}, volume = {115}, number = {8}, pages = {1760--1765}, month = feb } @article{vanderKamp:2010wp, author = {van der Kamp, M and Schaeffer, R and Jonsson, A}, title = {{Dynameomics: A Comprehensive Database of Protein Dynamics}}, journal = {Structure}, year = {2010} } @article{Blomberg:1997eu, author = {Blomberg, Niklas and Nilges, Michael}, title = {{Functional diversity of PH domains: an exhaustive modelling study}}, journal = {Folding Des.}, year = {1997}, volume = {2}, number = {6}, pages = {343--355}, month = dec } @article{Vihinen:1987jz, author = {Vihinen, Mauno}, title = {{Relationship of protein flexibility to thermostability}}, journal = {Protein Eng Des Sel}, year = {1987}, volume = {1}, number = {6}, pages = {477--480} } @article{Johner:2014hy, author = {Johner, Niklaus and Harries, Daniel and Khelashvili, George}, title = {{Curvature and Lipid Packing Modulate the Elastic Properties of Lipid Assemblies: Comparing H IIand Lamellar Phases}}, journal = {J. Phys. Chem. Lett.}, year = {2014}, volume = {5}, number = {23}, pages = {4201--4206}, month = dec } @article{Zhang:2015cl, author = {Zhang, Xiyun and Boccaletti, Stefano and Guan, Shuguang and Liu, Zonghua}, title = {{Explosive Synchronization in Adaptive and Multilayer Networks}}, journal = {Phys. Rev. Lett.}, year = {2015}, volume = {114}, number = {3}, pages = {038701}, month = jan } @article{Reuter:2003hg, author = {Reuter, N and Hinsen, K and Lacapere, J J}, title = {{The Nature of the Low-Frequency Normal Modes of the E1Ca Form of the SERCA1 Ca 2+-ATPase}}, journal = {Annals of the New York Academy of Sciences}, year = {2003}, volume = {986}, number = {1}, pages = {344--346}, month = apr } @article{Vertrees:2005jk, author = {Vertrees, Jason and Barritt, Phillip and Whitten, Steve and Hilser, Vincent J}, title = {{COREX/BEST server: a web browser-based program that calculates regional stability variations within protein structures.}}, journal = {Bioinformatics}, year = {2005}, volume = {21}, number = {15}, pages = {3318--3319}, month = aug } @webpage{Anonymous:_ltThrMS, title = {{PLOS Computational Biology: A Coarse-Grained Elastic Network Atom Contact Model and Its Use in the Simulation of Protein Dynamics and the Prediction of the Effect of Mutations}}, url = {http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003569} } @article{Lin:1998uz, author = {Lin, Y and Nielsen, R and Murray, D and Hubbell, W L and Mailer, C and Robinson, B H and Gelb, M H}, title = {{Docking phospholipase A2 on membranes using electrostatic potential-modulated spin relaxation magnetic resonance.}}, journal = {Science}, year = {1998}, volume = {279}, number = {5358}, pages = {1925--1929}, month = mar } @article{Anonymous:-DHHWTqF, title = {{assignment}}, year = {2005}, pages = {6} } @article{Skjaerven:2009bz, author = {Skjaerven, Lars and Hollup, Siv M and Reuter, Nathalie}, title = {{Normal mode analysis for proteins}}, journal = {Journal of Molecular Structure - Theochem}, year = {2009}, volume = {898}, number = {1-3}, pages = {42--48} } @webpage{Anonymous:ryrCruNM, title = {{Biosynthesis of phosphatidylcholine in bacteria}}, url = {http://www.sciencedirect.com/science/article/pii/S0163782702000504} } @article{Eichinger:1978de, author = {Eichinger, B E}, title = {{Scattering Functions for Gaussian Molecules. 2. Intermolecular Correlations}}, journal = {Macromolecules}, year = {1978}, volume = {11}, number = {5}, pages = {1056--1057}, month = sep } @article{Anonymous:rwXUksBz, title = {{Eigenvalues and Singular Values}}, year = {2008}, pages = {1--39}, month = feb } @article{Bartolucci:2005cd, author = {Bartolucci, Cecilia and Lamba, Doriano and Grazulis, Saulius and Manakova, Elena and Heumann, Hermann}, title = {{Crystal structure of wild-type chaperonin GroEL}}, journal = {J. Mol. Biol.}, year = {2005}, volume = {354}, number = {4}, pages = {940--951}, month = dec } @article{Zhang:2014gt, author = {Zhang, Leili and Yethiraj, Arun and Cui, Qiang}, title = {{Free Energy Calculations for the Peripheral Binding of Proteins/Peptides to an Anionic Membrane. 1. Implicit Membrane Models.}}, journal = {J Chem Theory Comput}, year = {2014}, volume = {10}, number = {7}, pages = {2845--2859}, month = jul } @article{Bravo:2001ua, author = {Bravo, J and Karathanassis, D and Pacold, C M and Pacold, M E and Ellson, C D and Anderson, K E and Butler, P J and Lavenir, I and Perisic, O and Hawkins, P T and Stephens, L and Williams, R L}, title = {{The crystal structure of the PX domain from p40(phox) bound to phosphatidylinositol 3-phosphate.}}, journal = {Mol. Cell}, year = {2001}, volume = {8}, number = {4}, pages = {829--839}, month = oct } @article{Walther:2004ut, author = {Walther, M and Wiesner, R and Kuhn, H}, title = {{Investigations into Calcium-dependent Membrane Association of 15-Lipoxygenase-1}}, journal = {J. Biol. Chem.}, year = {2004} } @article{Simossis:2005et, author = {Simossis, V A}, title = {{Homology-extended sequence alignment}}, journal = {Nucleic Acids Res.}, year = {2005}, volume = {33}, number = {3}, pages = {816--824}, month = feb } @article{Berg:2004jg, author = {Berg, J and Lassig, M}, title = {{Local graph alignment and motif search in biological networks}}, journal = {Proc. Natl. Acad. Sci. U. S. A.}, year = {2004}, volume = {101}, number = {41}, pages = {14689--14694} } @article{Yeh:2013wd, author = {{Yeh} and {Liu} and {Yu} and {Shih} and {Hwang} and Echave, Juli{\'a}n}, title = {{unpublished. PDF Proof: Mol. Biol. Evol.}}, year = {2013}, pages = {1--33}, month = may } @article{Calligari:2015bl, author = {Calligari, Paolo A and Calandrini, Vania and Ollivier, Jacques and Artero, Jean-Baptiste and H{\"a}rtlein, Michael and Johnson, Mark and Kneller, Gerald R}, title = {{Adaptation of Extremophilic Proteins with Temperature and Pressure: Evidence from Initiation Factor 6}}, journal = {J. Phys. Chem. B}, year = {2015}, volume = {119}, number = {25}, pages = {7860--7873}, month = jun } @webpage{Anonymous:pA2uO86a, title = {{PLOS Computational Biology: Novel Inhibitors Induce Large Conformational Changes of GAB1 Pleckstrin Homology Domain and Kill Breast Cancer Cells}}, url = {http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004021} } @article{Tama:2001uk, author = {Tama, F and Sanejouand, Y-H}, title = {{Conformational change of proteins arising from normal mode calculations}}, journal = {Protein Eng.}, year = {2001} } @article{Scouras:dh, author = {Scouras, Alexander D and Daggett, Valerie}, title = {{The dynameomics rotamer library: Amino acid side chain conformations and dynamics from comprehensive molecular dynamics simulations in water}}, journal = {Protein Sci.}, volume = {20}, number = {2}, pages = {341--352} } @article{Havugimana:2012is, author = {Havugimana, Pierre C and Hart, G Traver and Nepusz, Tam{\'a}s and Yang, Haixuan and Turinsky, Andrei L and Li, Zhihua and Wang, Peggy I and Boutz, Daniel R and Fong, Vincent and Phanse, Sadhna and Babu, Mohan and Craig, Stephanie A and Hu, Pingzhao and Wan, Cuihong and Vlasblom, James and Dar, Vaqaar-un-Nisa and Bezginov, Alexandr and Clark, Gregory W and Wu, Gabriel C and Wodak, Shoshana J and Tillier, Elisabeth R M and Paccanaro, Alberto and Marcotte, Edward M and Emili, Andrew}, title = {{A Census of Human Soluble Protein Complexes}}, journal = {Cell}, year = {2012}, volume = {150}, number = {5}, pages = {1068--1081}, month = aug } @article{Halle:2002wp, author = {Halle, Bertil}, title = {{Flexibility and packing in proteins}}, journal = {Proc. Natl. Acad. Sci. U. S. A.}, year = {2002}, volume = {99}, number = {3}, pages = {1274--1279}, month = feb } @article{Huber:2004wt, author = {Huber, Markus Ruschhaupt Wolfgang and Poustka, Annemarie and Mansmann, Ulrich}, title = {{Statistical Applications in Genetics and Molecular Biology}}, year = {2004}, pages = {1--26}, month = dec } @article{Ceruso:1999vw, author = {Ceruso, MA and Amadei, A and Nola, AD}, title = {{Mechanics and dynamics of B1 domain of protein G: role of packing and surface hydrophobic residues}}, journal = {PRS}, year = {1999}, volume = {8}, number = {01}, pages = {147--160} } @article{Anonymous:xynuDwyO, title = {{Matching}}, year = {2003}, pages = {6} } @article{Kastritis:2012hw, author = {Kastritis, P L and Bonvin, A M J J}, title = {{On the binding affinity of macromolecular interactions: daring to ask why proteins interact}}, journal = {Journal of The Royal Society Interface}, year = {2012}, volume = {10}, number = {79}, pages = {20120835--20120835}, month = nov } @article{Kim:1995wo, author = {Kim, Y T and Muramatsu, T and Takahashi, K}, title = {{Identification of Trp300 as an important residue for Escherichia coli leader peptidase activity.}}, journal = {Eur. J. Biochem.}, year = {1995}, volume = {234}, number = {1}, pages = {358--362}, month = nov } @webpage{SarahBelia:2008dg, author = {Sarah Belia, Fiona Fidler Jennifer Williams and Geoff Cumming}, title = {{Researchers Misunderstand Confidence Intervals and Standard Error Bars }}, year = {2008}, month = nov } @article{Sokolova:2009vu, author = {Sokolova, Marina and Lapalme, Guy}, title = {{A systematic analysis of performance measures for classification tasks}}, journal = {Information Processing {\&} Management}, year = {2009}, volume = {45}, number = {4}, pages = {427--437} } @article{Eyal:2006bd, author = {Eyal, Eran and Yang, Lee-Wei and Bahar, Ivet}, title = {{Anisotropic network model: systematic evaluation and a new web interface}}, journal = {Bioinformatics}, year = {2006}, volume = {22}, number = {21}, pages = {2619--2627}, month = aug } @article{Elazar:2016jh, author = {Elazar, Assaf and Weinstein, Jonathan Jacob and Prilusky, Jaime and Fleishman, Sarel Jacob}, title = {{Interplay between hydrophobicity and the positive-inside rule in determining membrane-protein topology}}, journal = {Proc. Natl. Acad. Sci. U. S. A.}, year = {2016}, volume = {113}, number = {37}, pages = {10340--10345}, month = sep } @article{Jepson:2001vk, author = {Jepson, M and Bullifent, H L and Crane, D and Flores-Diaz, M and Alape-Giron, A and Jayasekeera, P and Lingard, B and Moss, D and Titball, R W}, title = {{Tyrosine 331 and phenylalanine 334 in Clostridium perfringens alpha-toxin are essential for cytotoxic activity.}}, journal = {Febs Lett}, year = {2001}, volume = {495}, number = {3}, pages = {172--177}, month = apr } @article{Sanderson:2005jj, author = {Sanderson, John M}, title = {{Peptide?lipid interactions: insights and perspectives}}, journal = {Org. Biomol. Chem.}, year = {2005}, volume = {3}, number = {2}, pages = {201} } @article{Tehver:2009if, author = {Tehver, Riina and Chen, Jie and Thirumalai, D}, title = {{Allostery Wiring Diagrams in the Transitions that Drive the GroEL Reaction Cycle}}, journal = {J. Mol. Biol.}, year = {2009}, volume = {387}, number = {2}, pages = {390--406} } @article{Tama:2011gc, author = {Tama, F and Valle, M and Frank, J and Brooks, C L}, title = {{Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy}}, journal = {Proc. Natl. Acad. Sci. U. S. A.}, year = {2011}, volume = {100}, number = {16}, pages = {9319--9323}, month = may } @article{Stahelin:2003is, author = {Stahelin, Robert V and Long, Fei and Peter, Brian J and Murray, Diana and De Camilli, Pietro and McMahon, Harvey T and Cho, Wonhwa}, title = {{Contrasting Membrane Interaction Mechanisms of AP180 N-terminal Homology (ANTH) and Epsin N-terminal Homology (ENTH) Domains}}, journal = {J. Biol. Chem.}, year = {2003}, volume = {278}, number = {31}, pages = {28993--28999}, month = jul } @article{Crowell:QAJhRPwk, author = {Crowell, Benjamin}, title = {{Vibrations_and_Waves_B_Crowell}}, year = {2006}, pages = {106}, month = dec } @article{Laskowski:2008ho, author = {Laskowski, Roman A and Thornton, Janet M}, title = {{Understanding the molecular machinery of genetics through 3D structures}}, journal = {Nat Rev Genet}, year = {2008}, volume = {2008}, number = {2}, pages = {141--151}, month = feb } @article{Tobi:2012dg, author = {Tobi, Dror}, title = {{Dynamics alignment: Comparison of protein dynamics in the scop database}}, journal = {Proteins: Struct., Funct., Bioinf.}, year = {2012}, volume = {80}, number = {4}, pages = {1167--1176}, month = feb } @article{Fidelak:2010gc, author = {Fidelak, Jeremy and Ferrer, Silvia and Oberlin, Michael and Moras, Dino and Dejaegere, Annick and Stote, Roland H}, title = {{Dynamic correlation networks in human peroxisome proliferator-activated receptor-$\gamma$ nuclear receptor protein}}, journal = {Eur Biophys J}, year = {2010}, pages = {1--10}, month = may } @article{Osgood:2009tv, author = {Osgood, Brad}, title = {{Lecture notes - The fourier Transform and its Applications}}, year = {2009}, pages = {1--428}, month = aug } @webpage{GOWERS:te, author = {GOWERS, W.T.}, title = {{THE WORK OF ENDRE SZEMER{\'E}DI}}, url = {http://gowers.files.wordpress.com/2012/03/talktalk2.pdf} } @article{Kantari:2009uf, author = {Kantari, Chahrazade and Gabillet, Julie and Hajjar, Eric and Reuter, Nathalie and Witko-Sarsat, Veronique}, title = {{Mutagenesis analysis of the insertion domain of proteinase 3 into membrane: a potential target for anti-inflammatory therapy in vasculitis}}, journal = {Apmis}, year = {2009}, volume = {117}, pages = {121--121} } @article{Anonymous:2013tu, title = {{Lipid properties in mebranes}}, year = {2013}, pages = {1--12}, month = jun } @article{Stahelin:2001cr, author = {Stahelin, Robert V and Cho, Wonhwa}, title = {{Differential Roles of Ionic, Aliphatic, and Aromatic Residues in Membrane{\textminus}Protein Interactions:~ A Surface Plasmon Resonance Study on Phospholipases A 2{\dag}}}, journal = {Biochemistry}, year = {2001}, volume = {40}, number = {15}, pages = {4672--4678}, month = apr } @article{Kunsch:1989ws, author = {Kunsch, HR}, title = {{The jackknife and the bootstrap for general stationary observations}}, journal = {The Annals of Statistics}, year = {1989}, pages = {1217--1241} } @article{LindorffLarsen:2005bi, author = {Lindorff-Larsen, Kresten and Best, Robert B and Depristo, Mark A and Dobson, Christopher M and Vendruscolo, Michele}, title = {{Simultaneous determination of protein structure and dynamics.}}, journal = {Nature}, year = {2005}, volume = {433}, number = {7022}, pages = {128--132}, month = jan } @article{Berman:2000fma, author = {Berman, Helen M and Westbrook, John and Feng, Zukang and Gilliland, Gary and Bhat, T N and Weissig, Helge and Shindyalov, Ilya N and Bourne, Philip E}, title = {{The Protein Data Bank}}, journal = {Nucleic Acids Res.}, year = {2000}, volume = {28}, number = {1}, pages = {235--242}, month = jan } @article{Tiwary:2013tg, author = {Tiwary, Pratyush and Parrinello, Michele}, title = {{From Metadynamics to Dynamics}}, journal = {arXiv}, year = {2013}, month = sep } @article{Zhang:2006hb, author = {Zhang, Chun-Mei and Perona, John J and Ryu, Kang and Francklyn, Christopher and Hou, Ya-Ming}, title = {{Distinct kinetic mechanisms of the two classes of aminoacyl-tRNA synthetases}}, journal = {J. Mol. Biol.}, year = {2006}, volume = {361}, number = {2}, pages = {300--311} } @article{Jarosch:2005io, author = {Jarosch, R}, title = {{The alpha-helix, an overlooked molecular motor}}, journal = {Protoplasma}, year = {2005}, volume = {227}, number = {1}, pages = {37--46}, month = dec } @inproceedings{Parulek:2012iw, author = {Parulek, Julius and Turkay, Cagatay and Reuter, Nathalie and Viola, Ivan}, title = {{Implicit surfaces for interactive graph based cavity analysis of molecular simulations}}, booktitle = {2012 IEEE Symposium on Biological Data Visualization (BioVis)}, year = {2012}, pages = {115--122}, publisher = {IEEE} } @article{Zhao:2006ic, author = {Zhao, Gang and London, Erwin}, title = {{An amino acid {\textquotedblleft}transmembrane tendency{\textquotedblright} scale that approaches the theoretical limit to accuracy for prediction of transmembrane helices: Relationship to biological hydrophobicity}}, journal = {Protein Sci.}, year = {2006}, volume = {15}, number = {8}, pages = {1987--2001}, month = aug } @article{LeoMacias:2005cy, author = {Leo-Macias, Alejandra and Lopez-Romero, Pedro and Lupyan, Dmitry and Zerbino, Daniel and Ortiz, Angel R}, title = {{Core deformations in protein families: a physical perspective}}, journal = {Biophys. Chem.}, year = {2005}, volume = {115}, number = {2-3}, pages = {125--128}, month = apr } @article{Yorke:2014bd, author = {Yorke, Briony A and Beddard, Godfrey S and Owen, Robin L and Pearson, Arwen R}, title = {{time-resolved crystallography using the hadamard transform}}, journal = {Nature Methods}, year = {2014}, pages = {1--6}, month = oct } @article{Shlesinger:2009bp, author = {Shlesinger, Michael F}, title = {{Random searching}}, journal = {J. Phys. A: Math. Theor.}, year = {2009}, volume = {42}, number = {43}, pages = {434001}, month = oct } @article{Brandl:1986wc, author = {Brandl, CJ and Deber, CM}, title = {{Hypothesis about the function of membrane-buried proline residues in transport proteins}}, journal = {Proc. Natl. Acad. Sci. U. S. A.}, year = {1986}, volume = {83}, number = {4}, pages = {917} } @article{Ming:2002kw, author = {Ming, D and Kong, Y and Wu, Y and Ma, J}, title = {{Substructure synthesis method for simulating large molecular complexes}}, journal = {Proc. Natl. Acad. Sci. U. S. A.}, year = {2002}, volume = {100}, number = {1}, pages = {104--109}, month = dec } @article{Xie:2008gk, author = {Xie, Lei and Bourne, Philip E}, title = {{Detecting evolutionary relationships across existing fold space, using sequence order-independent profile-profile alignments}}, journal = {Proc. Natl. Acad. Sci. U. S. A.}, year = {2008}, volume = {105}, number = {14}, pages = {5441--5446} } @article{Boldo:2012tf, author = {Boldo, Sylvie and Cl{\'e}ment, Fran{\c c}ois and Filli{\^a}tre, Jean-Christophe and Mayero, Micaela and Melquiond, Guillaume and Weis, Pierre}, title = {{Trusting Computations: a Mechanized Proof from Partial Differential Equations to Actual Program}}, year = {2012}, month = dec } @article{Chandonia:2004eh, author = {Chandonia, John-Marc and Hon, Gary and Walker, Nigel S. and Lo Conte, Loredana and Koehl, Patrice and Levitt, Michael and Brenner, SE}, title = {{The ASTRAL Compendium in 2004}}, journal = {Nucleic Acids Res.}, year = {2004}, volume = {32}, pages = {D189--D192} } @article{Bose:1938ti, author = {Bose, R C and Roy, S N}, title = {{The Distribution of the Studentised D{\texttwosuperior}-Statistic}}, journal = {Sankhy{\=a}: The Indian Journal of Statistics (1933-1960)}, year = {1938}, volume = {4}, number = {1}, pages = {19--38}, month = jan } @article{Anonymous:U4O1_GsE, title = {{Mechanisms of protein oligomerization, the critical role of insertions and deletions in maintaining different oligomeric states}} } @article{Merz:1991je, author = {Merz, Kenneth M}, title = {{Carbon dioxide binding to human carbonic anhydrase II}}, journal = {JACS}, year = {1991}, volume = {113}, number = {2}, pages = {406--411}, month = jan } @article{Sonego:2008gp, author = {Sonego, Paolo and Kocsor, Andr{\'a}s and Pongor, S{\'a}ndor}, title = {{ROC analysis: applications to the classification of biological sequences and 3D structures.}}, journal = {Brief. Bioinformatics}, year = {2008}, volume = {9}, number = {3}, pages = {198--209}, month = may } @article{BalaliMood:2009cv, author = {Balali-Mood, Kia and Bond, Peter J and Sansom, Mark S P}, title = {{Interaction of Monotopic Membrane Enzymes with a Lipid Bilayer: A Coarse-Grained MD Simulation Study {\dag}}}, journal = {Biochemistry}, year = {2009}, volume = {48}, number = {10}, pages = {2135--2145}, month = mar } @article{Shakhnovich:1996vo, author = {Shakhnovich, E and Abkevich, V and Ptitsyn, O}, title = {{Conserved residues and the mechanism of protein folding}}, journal = {Nature}, year = {1996}, volume = {379}, number = {6560}, pages = {96--98} } @article{Kutateladze:1999fm, author = {Kutateladze, Tatiana G and Ogburn, Kenyon D and Watson, William T and de Beer, Tonny and Emr, Scott D and Burd, Christopher G and Overduin, Michael}, title = {{Phosphatidylinositol 3-Phosphate Recognition by the FYVE Domain}}, journal = {Mol. Cell}, year = {1999}, volume = {3}, number = {6}, pages = {805--811}, month = jun } @article{Shenkarev:2006fg, author = {Shenkarev, Zakhar O and Nadezhdin, Kirill D and Sobol, Vladimir A and Sobol, Alexander G and Skjeldal, Lars and Arseniev, Alexander S}, title = {{Conformation and mode of membrane interaction in cyclotides. Spatial structure of kalata B1 bound to a dodecylphosphocholine micelle.}}, journal = {Febs J}, year = {2006}, volume = {273}, number = {12}, pages = {2658--2672}, month = jun } @webpage{Anonymous:nL_7uEiK, title = {{Phys. Rev. Lett. 115, 108102 (2015) - Enhanced Diffusion of Enzymes that Catalyze Exothermic Reactions}}, url = {http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.115.108102} } @article{Skjaerven:2012fu, author = {Skjaerven, Lars and Muga, Arturo and Reuter, Nathalie and Martinez, Aurora}, title = {{A dynamic model of long-range conformational adaptations triggered by nucleotide binding in GroEL-GroES}}, journal = {Proteins: Struct., Funct., Bioinf.}, year = {2012}, volume = {80}, pages = {2333--2346} } @article{Wu:2007uu, author = {Wu, X and Kumar, V and Quinlan, JR and Ghosh, J and Yang, Q}, title = {{Tor 10 algorithms in data mining}}, year = {2007} } @article{Anonymous:vS6QApXi, title = {{matching}}, year = {2007}, pages = {10} } @article{Hasegawa:2009kc, author = {Hasegawa, Hitomi and Holm, Liisa}, title = {{Advances and pitfalls of protein structural alignment}}, journal = {Current Opinion in Structural Biology}, year = {2009}, volume = {19}, number = {3}, pages = {341--348} } @article{Nepomnyachiy:2014dz, author = {Nepomnyachiy, Sergey and Ben-Tal, Nir and Kolodny, Rachel}, title = {{Global view of the protein universe}}, journal = {Proc. Natl. Acad. Sci. U. S. A.}, year = {2014}, volume = {111}, number = {32}, pages = {11691--11696}, month = aug } @article{Barber:2014ff, author = {Barber, M F and Elde, N C}, title = {{Escape from bacterial iron piracy through rapid evolution of transferrin}}, journal = {Science}, year = {2014}, volume = {346}, number = {6215}, pages = {1362--1366}, month = dec } @phdthesis{Fuglebakk:2013vk, author = {Fuglebakk, Edvin}, title = {{Methods for comparative analysis of the intrinsic motions of computational protein models}}, school = {University of Bergen}, year = {2013}, address = {Department of Informatics, University of Bergen}, month = apr } @article{Skjaerven:2011gr, author = {Skjaerven, Lars and Reuter, Nathalie and Martinez, Aurora}, title = {{Dynamics, flexibility and ligand-induced conformational changes in biological macromolecules: a computational approach.}}, journal = {Future Med Chem}, year = {2011}, volume = {3}, number = {16}, pages = {2079--2100}, month = dec } @article{Lampe:2007wn, author = {Lampe, Ove Daae and Viola, Ivan and Reuter, Nathalie and Hauser, Helwig}, title = {{Two-level approach to efficient visualization of protein dynamics}}, journal = {Ieee T Vis Comput Gr}, year = {2007}, volume = {13}, number = {6}, pages = {1616--1623} } @article{Romo:2011ey, author = {Romo, Tod D. and Grossfield, Alan}, title = {{Validating and improving elastic network models with molecular dynamics simulations}}, journal = {Proteins: Struct., Funct., Bioinf.}, year = {2011}, volume = {79}, number = {1}, pages = {23--34} } @article{Petit:2009gh, author = {Petit, Chad M and Zhang, Jun and Sapienza, Paul J and Fuentes, Ernesto J and Lee, Andrew L}, title = {{Hidden dynamic allostery in a PDZ domain.}}, journal = {Proc. Natl. Acad. Sci. U. S. A.}, year = {2009}, volume = {106}, number = {43}, pages = {18249--18254}, month = oct } @incollection{Carnevale:2010ku, author = {Carnevale, Vincenzo and Micheletti, Cristian and Pontiggia, Francesco and Potestio, Raffaello}, title = {{Bridging the Atomic and Coarse-Grained Descriptions of Collective Motions in Proteins}}, booktitle = {apps.webofknowledge.com}, year = {2010}, pages = {159--178}, publisher = {Springer New York}, address = {New York, NY} } @article{Hong:2013bk, author = {Hong, Liang and Glass, Dennis and Nickels, Jonathan and Perticaroli, Stefania and Yi, Zheng and Madhusudan, Tyagi and O{\textquoteright}Neill, Hugh and Zhang, Qiu and Sokolov, Alexei and Smith, Jeremy}, title = {{Elastic and Conformational Softness of a Globular Protein}}, journal = {Phys. Rev. Lett.}, year = {2013}, volume = {110}, number = {2}, pages = {028104}, month = jan } @article{Antonny:2011jn, author = {Antonny, Bruno}, title = {{Mechanisms of Membrane Curvature Sensing}}, journal = {Annu Rev Biochem}, year = {2011}, volume = {80}, number = {1}, pages = {101--123}, month = jul } @article{Dalpadado:2012dg, author = {Dalpadado, Padmini and Ingvaldsen, Randi B and Stige, Leif Christian and Bogstad, Bjarte and Knutsen, Tor and Ottersen, Geir and Ellertsen, Bj{\o}rnar}, title = {{Climate effects on Barents Sea ecosystem dynamics}}, journal = {ICES J. Mar. Sci.}, year = {2012}, volume = {69}, number = {7}, pages = {1303--1316}, month = sep } @article{Haliloglu:2008kv, author = {Haliloglu, Turkan and Seyrek, Emek and Erman, Burak}, title = {{Prediction of Binding Sites in Receptor-Ligand Complexes with the Gaussian Network Model}}, journal = {Phys. Rev. Lett.}, year = {2008}, volume = {100}, number = {22}, pages = {4}, month = jun } @article{Harrison:2009uf, author = {Harrison, N M}, title = {{An INtroduction ot Density Functinoal Theory}}, year = {2009}, pages = {1--26}, month = dec } @webpage{Anonymous:CpoIrehv, title = {{Phys. Rev. Lett. 113, 238701 (2014) - Universal Power Law Governing Pedestrian Interactions}}, url = {http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.113.238701} } @article{Taylor:2009eo, author = {Taylor, William R and Chelliah, Vijayalakshmi and Hollup, Siv Midtun and MacDonald, James T and Jonassen, Inge}, title = {{Probing the "Dark Matter" of Protein Fold Space}}, journal = {Structure}, year = {2009}, volume = {17}, number = {9}, pages = {1244--1252} } @article{Hollup:2008ui, author = {Hollup, S M and Taylor, W R and Jonassen, I}, title = {{Structural Fragments in Protein Model Refinement}}, journal = {Protein Peptide Lett}, year = {2008}, volume = {15}, number = {9}, pages = {964--971}, month = sep } @article{Gerek:2011kq, author = {Gerek, Z Nevin ZN and Ozkan, S Banu SB}, title = {{Change in allosteric network affects binding affinities of PDZ domains: analysis through perturbation response scanning.}}, journal = {PLoS Comput. Biol.}, year = {2011}, volume = {7}, number = {10}, pages = {e1002154--e1002154}, month = sep } @article{Provost:1997th, author = {Provost, Foster and Fawcett, Tom}, title = {{Analysis and Vizualzation of Classifier Performance: Comparison under Imprecise Class and Cost Distributions}}, year = {1997}, pages = {1--6} } @article{Anonymous:cvvUsIf6, title = {{stochastic_dynamics}}, year = {2003}, pages = {1--4}, month = oct } @article{Bhardwaj:2007gz, author = {Bhardwaj, N and Stahelin, R V and Zhao, G and Cho, W and Lu, H}, title = {{MeTaDoR: a comprehensive resource for membrane targeting domains and their host proteins}}, journal = {Bioinformatics}, year = {2007}, volume = {23}, number = {22}, pages = {3110--3112}, month = nov } @article{Edidin:2001jj, author = {Edidin, Michael}, title = {{Membrane Cholesterol, Protein Phosphorylation, and Lipid Rafts}}, journal = {Sci. Signal.}, year = {2001}, volume = {2001}, number = {67}, pages = {pe1--pe1}, month = jan } @article{Bihr:2014ks, author = {Bihr, Timo and Fenz, Susanne and Sackmann, Erich and Merkel, Rudolf and Seifert, Udo and Sengupta, Kheya and Smith, Ana-Sun{\v c}ana}, title = {{Association Rates of Membrane-Coupled Cell Adhesion Molecules}}, journal = {Biophys. J.}, year = {2014}, volume = {107}, number = {11}, pages = {L33--L36}, month = dec } @article{Stephenson:2004vj, author = {Stephenson, David}, title = {{XML Schema best practices}}, year = {2004}, pages = {1--18}, month = dec } @article{Loytynoja:2008ku, author = {Loytynoja, A and Goldman, N}, title = {{Phylogeny-Aware Gap Placement Prevents Errors in Sequence Alignment and Evolutionary Analysis}}, journal = {Science}, year = {2008}, volume = {320}, number = {5883}, pages = {1632--1635}, month = jun } @article{Markwick:2012fu, author = {Markwick, Phineus R L and Nilges, Michael}, title = {{Computational approaches to the interpretation of NMR data for studying protein dynamics}}, journal = {Chem. Phys.}, year = {2012}, volume = {396}, pages = {124--134}, month = mar } @article{Echeverria:2014em, author = {Echeverria, Ignacia and Makarov, Dmitrii E and Papoian, Garegin A}, title = {{Concerted Dihedral Rotations Give Rise to Internal Friction in Unfolded Proteins}}, journal = {JACS}, year = {2014}, volume = {136}, number = {24}, pages = {8708--8713}, month = jun } @article{Echave:2010vk, author = {Echave, Julian}, title = {{On one right way of reducing the dimensionality to compare covariance matrices
}}, year = {2010}, pages = {1--4}, month = jun } @article{Kwan:2011jo, author = {Kwan, Ann H AH and Mobli, Mehdi M and Gooley, Paul R PR and King, Glenn F GF and Mackay, Joel P JP}, title = {{Macromolecular NMR spectroscopy for the non-spectroscopist.}}, journal = {Febs J}, year = {2011}, volume = {278}, number = {5}, pages = {687--703}, month = feb } @article{Mattingly:2018jka, author = {Mattingly, Henry H and Transtrum, Mark K and Abbott, Michael C and Machta, Benjamin B}, title = {{Maximizing the information learned from finite data selects a simple model}}, journal = {Proc Natl Acad Sci U S A}, year = {2018}, volume = {115}, number = {8}, pages = {1760--1765}, month = feb } @article{Whitmore:2010hw, author = {Whitmore, L and Woollett, B and Miles, A J and Klose, D P and Janes, R W and Wallace, B A}, title = {{PCDDB: the protein circular dichroism data bank, a repository for circular dichroism spectral and metadata}}, journal = {Nucleic Acids Res.}, year = {2010}, volume = {39}, number = {Database}, pages = {D480--D486}, month = dec } @article{Huang:2014kn, author = {Huang, Rui and Yamamoto, Kazutoshi and Zhang, Meng and Popovych, Nataliya and Hung, Ivan and Im, Sang-Choul and Gan, Zhehong and Waskell, Lucy and Ramamoorthy, Ayyalusamy}, title = {{Probing the Transmembrane Structure and Dynamics of Microsomal NADPH-cytochrome P450 oxidoreductase by Solid-State NMR}}, journal = {Biophys. J.}, year = {2014}, volume = {106}, number = {10}, pages = {2126--2133}, month = may } @article{AlBluwi:2012gl, author = {Al-Bluwi, Ibrahim and Sim{\'e}on, Thierry and Cort{\'e}s, Juan}, title = {{Motion planning algorithms for molecular simulations: A survey}}, journal = {Computer Science Review}, year = {2012}, volume = {6}, number = {4}, pages = {125--143}, month = jul } @article{Mendez:2010tw, author = {M{\'e}ndez, Raul and Bastolla, Ugo}, title = {{Torsional network model: normal modes in torsion angle space better correlate with conformation changes in proteins.}}, journal = {Phys. Rev. Lett.}, year = {2010}, volume = {104}, number = {22}, pages = {228103(4)} } @article{Mason:2002tba, author = {Mason, SJ and Graham, NE}, title = {{Areas beneath the relative operating characteristics (ROC) and relative operating levels (ROL) curves: Statistical significance and interpretation}}, journal = {Q J Roy Meteor Soc}, year = {2002}, volume = {128}, number = {584}, pages = {2145--2166} } @article{Madhusudhan:2009ho, author = {Madhusudhan, MS and Webb, B M and Marti-Renom, M A and Eswar, N and Sali, A}, title = {{Alignment of multiple protein structures based on sequence and structure features}}, journal = {Protein Eng Des Sel}, year = {2009}, volume = {22}, number = {9}, pages = {569--574}, month = sep } @article{Lupyan:2005gh, author = {Lupyan, D}, title = {{A new progressive-iterative algorithm for multiple structure alignment}}, journal = {Bioinformatics}, year = {2005}, volume = {21}, number = {15}, pages = {3255--3263}, month = jun } @incollection{Malliavin:2012go, author = {Malliavin, Th{\'e}r{\`e}se E and Mucherino, Antonio and Nilges, Michael}, title = {{Distance Geometry in Structural Biology: New Perspectives}}, year = {2012}, pages = {329--350}, publisher = {Springer New York}, address = {New York, NY}, month = nov } @article{Cao:uh, author = {Cao, Jian and Burke, John E and Dennis, Edward A}, title = {{Using Hydrogen/Deuterium Exchange Mass Spectrometry to Define the Specific Interactions of the Phospholipase A2 Superfamily with Lipid Substrates, Inhibitors, and Membranes}}, journal = {jbc.org} } @article{Brannstrom:2005kh, author = {Br{\"a}nnstr{\"o}m, {\AA} and Sumpter, D J T}, title = {{The role of competition and clustering in population dynamics}}, journal = {Proceedings of the Royal Society of London B: Biological Sciences}, year = {2005}, volume = {272}, number = {1576}, pages = {2065--2072}, month = oct } @article{Halskau:2009cb, author = {Halskau, O and Ying, M and Baumann, A and Kleppe, R and Rodriguez-Larrea, D and Almas, B and Haavik, J and Martinez, A}, title = {{Three-way Interaction between 14-3-3 Proteins, the N-terminal Region of Tyrosine Hydroxylase, and Negatively Charged Membranes}}, journal = {J. Biol. Chem.}, year = {2009}, volume = {284}, number = {47}, pages = {32758--32769}, month = nov } @article{Zen:2009hi, author = {Zen, Andrea and de Chiara, Cesira and Pastore, Annalisa and Micheletti, Cristian}, title = {{Using dynamics-based comparisons to predict nucleic acid binding sites in proteins: an application to OB-fold domains.}}, journal = {Bioinformatics}, year = {2009}, volume = {25}, number = {15}, pages = {1876--1883}, month = aug } @article{Krissinel:2007wq, author = {Krissinel, E and Henrick, K}, title = {{Inference of macromolecular assemblies from crystalline state}}, journal = {J. Mol. Biol.}, year = {2007} } @article{OpdenKamp:1979un, author = {Op den Kamp, Jos A F}, title = {{LIPID ASYMMETRY IN MEBRANES}}, journal = {Ann. Rev. Bichem.}, year = {1979}, pages = {47--71} } @article{Zhou:1993vk, author = {Zhou, H X}, title = {{Brownian dynamics study of the influences of electrostatic interaction and diffusion on protein-protein association kinetics.}}, journal = {Biophys. J.}, year = {1993}, volume = {64}, number = {6}, pages = {1711}, month = jun } @article{Rivoire:vr, author = {Rivoire, Olivier and Leibler, Stanislas}, title = {{A model for the generation and transmission of variations in evolution}}, journal = {pnas.org} } @article{Sippl:2008ec, author = {Sippl, Manfred J and Suhrer, Stefan J and Gruber, Markus and Wiederstein, Markus}, title = {{A discrete view on fold space}}, journal = {Bioinformatics}, year = {2008}, volume = {24}, number = {6}, pages = {870--871} } @article{Nehrt:2011tj, author = {Nehrt, Nathan L and Clark, Wyatt T and Radivojac, Predrag and Hahn, Matthew W}, title = {{Testing the Ortholog Conjecture with Comparative Functional Genomic Data from Mammals}}, journal = {PLoS Comput. Biol.}, year = {2011}, volume = {7}, number = {6}, pages = {e1002073}, month = jun } @article{Go:1969dk, author = {Go, Nobuhiro}, title = {{Analysis of the Contribution of Internal Vibrations to the Statistical Weights of Equilibrium Conformations of Macromolecules}}, journal = {J. Chem. Phys.}, year = {1969}, volume = {51}, number = {11}, pages = {4751} } @article{Bahar:1998wo, author = {Bahar, I and Atilgan, AR and Demirel, MC and Erman, B}, title = {{Vibrational dynamics of folded proteins: significance of slow and fast motions in relation to function and stability}}, journal = {Phys. Rev. Lett.}, year = {1998}, volume = {80}, number = {12}, pages = {2733--2736} } @article{Hedin:2002eu, author = {Hedin, Eva M K and H{\o}yrup, Pernille and Patkar, Shamkant A and Vind, Jesper and Svendsen, Allan and Fransson, Linda and Hult, Karl}, title = {{Interfacial Orientation of Thermomyces lanuginosaLipase on Phospholipid Vesicles Investigated by Electron Spin Resonance Relaxation Spectroscopy {\dag}}}, journal = {Biochemistry}, year = {2002}, volume = {41}, number = {48}, pages = {14185--14196}, month = dec } @article{Seckler:2013de, author = {Seckler, James M and Leioatts, Nicholas and Miao, Hongyu and Grossfield, Alan}, title = {{The interplay of structure and dynamics: Insights from a survey of HIV-1 reverse transcriptase crystal structures}}, journal = {Proteins: Struct., Funct., Bioinf.}, year = {2013}, volume = {81}, number = {10}, pages = {1792--1801}, month = aug } @article{HOLM:1996te, author = {HOLM, L and SANDER, C}, title = {{Mapping the protein universe}}, journal = {Science}, year = {1996}, volume = {273}, number = {5275}, pages = {595--602} } @article{Bahar:1997um, author = {Bahar, Ivet and Jernigan, R L}, title = {{Inter-residue potentials in globular proteins and the dominance of highly specific hydrophilic interactions at close separation}}, journal = {J. Mol. Biol.}, year = {1997}, volume = {266}, number = {1}, pages = {195--214} } @article{Derenyi:2015gz, author = {Der{\'e}nyi, Imre and Sz{\"o}ll{\H o}si, Gergely J}, title = {{Effective Temperature of Mutations}}, journal = {Phys. Rev. Lett.}, year = {2015}, volume = {114}, number = {5}, pages = {058101}, month = feb } @article{Hwang:2010dh, author = {Hwang, Howook and Vreven, Thom and Janin, Jo{\"e}l and Weng, Zhiping}, title = {{Protein-protein docking benchmark version 4.0.}}, journal = {Proteins: Struct., Funct., Bioinf.}, year = {2010}, volume = {78}, number = {15}, pages = {3111--3114}, month = nov } @article{Akutsu:2000ua, author = {Akutsu, T and Halldorsson, MM}, title = {{On the approximation of largest common subtrees and largest common point sets}}, journal = {Theor Comput Sci}, year = {2000}, volume = {233}, pages = {33--50} } @article{Gribskov:1996ur, author = {Gribskov, Michael and Robinson, Nina L.}, title = {{Use of receiver operating characteristic (ROC) analysis to evaluate sequence matching}}, journal = {Comput Chem}, year = {1996}, volume = {20}, number = {1}, pages = {25--33} } @unpublished{Fuglebakk:2013vv, author = {Fuglebakk, Edvin and Tiwari, Sandhya and Hollup, Siv Midtun and Cragnolini, Tristan and Skjaerven, Lars and Grindhaug, Svenn Helge and Kidane, Tekle and Reuter, Nathalie}, title = {{Comparing protein structure flexibility using WEBnm@ v2.0}} } @article{Reuveni:2008dv, author = {Reuveni, Shlomi and Granek, Rony and Klafter, Joseph}, title = {{Proteins: Coexistence of stability and flexibility}}, journal = {Phys. Rev. Lett.}, year = {2008}, volume = {100}, number = {20}, pages = {208101}, month = may } @webpage{Anonymous:KdBBY6EO, title = {{PLOS Computational Biology: Diffusion, Crowding {\&} Protein Stability in a Dynamic Molecular Model of the Bacterial Cytoplasm}}, url = {http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000694} } @article{Minitti:2015ut, author = {Minitti, M P and Budarz, J M and Kirrander, A and Robinson, J S and Ratner, D and Lane, T J and Zhu, D and Glownia, J M and Kozina, M and Lemke, H T and Sikorski, M and Feng, Y and Nelson, S and Saita, K and Stankus, B and Northey, T and Hastings, J B and Weber, P M}, title = {{Imaging Molecular Motion: Femtosecond X-Ray Scattering of an Electrocyclic Chemical Reaction.}}, journal = {Phys. Rev. Lett.}, year = {2015}, volume = {114}, number = {25}, pages = {255501}, month = jun } @article{Konagurthu:2006fq, author = {Konagurthu, Arun S and Whisstock, James C and Stuckey, Peter J and Lesk, Arthur M.}, title = {{MUSTANG: a multiple structural alignment algorithm.}}, journal = {Proteins: Struct., Funct., Bioinf.}, year = {2006}, volume = {64}, number = {3}, pages = {559--574}, month = aug } @webpage{Anonymous:tUrJhhdt, title = {{Formal Methods in CafeOBJ}}, url = {http://download.springer.com/static/pdf/366/chp%253A10.1007%252F3-540-45788-7_1.pdf?originUrl=http%3A%2F%2Flink.springer.com%2Fchapter%2F10.1007%2F3-540-45788-7_1&token2=exp=1472024530~acl=%2Fstatic%2Fpdf%2F366%2Fchp%25253A10.1007%25252F3-540-45788-7_1.pdf%3ForiginUrl%3Dhttp%253A%252F%252Flink.springer.com%252Fchapter%252F10.1007%252F3-540-45788-7_1*~hmac=ba5a77f6298d897cad9cc0923d6815f67f1db2a484e27e6b560567ac6d6b5232} } @webpage{Anonymous:pX5eHEin, title = {{Energetics of side-chain snorkeling in transmembrane helices probed by nonproteinogenic amino acids}}, url = {http://www.pnas.org/content/113/38/10559.full} } @article{Bastolla:2003kd, author = {Bastolla, U and Porto, M and Roman, HE and Vendruscolo, M}, title = {{Statistical properties of neutral evolution}}, journal = {Journal of Molecular Evolution}, year = {2003}, volume = {57}, pages = {S103--S119} } @article{DelCampo:2014go, author = {Del Campo, Claudia M and Mishra, Ashwini K and Wang, Yu-Hsiu and Roy, Craig R and Janmey, Paul A and Lambright, David G}, title = {{Structural Basis for PI(4)P-Specific Membrane Recruitment of the Legionella pneumophila Effector DrrA/SidM}}, journal = {Structure}, year = {2014}, volume = {22}, number = {3}, pages = {397--408}, month = mar } @article{Robinson:2008hw, author = {Robinson, John M}, title = {{Physical Limits on Computation by Assemblies of Allosteric Proteins}}, journal = {Phys. Rev. Lett.}, year = {2008}, volume = {101}, number = {17}, pages = {4}, month = oct } @article{LandoltMarticorena:1993kg, author = {Landolt-Marticorena, Carolina and Williams, Karen A and Deber, Charles M and Reithmeier, Reinhart A F}, title = {{Non-random Distribution of Amino Acids in the Transmembrane Segments of Human Type I Single Span Membrane Proteins}}, journal = {J. Mol. Biol.}, year = {1993}, volume = {229}, number = {3}, pages = {602--608}, month = feb } @article{Suzuki:2011wi, author = {Suzuki, KGN and Kasai, R S and Ritchie, K and Fujiwara, T K}, title = {{Hierarchical mesoscale domain organization of the plasma membrane}}, journal = {Trends in biochemical {\ldots}}, year = {2011} } @article{Brinkmann:2004bx, author = {Brinkmann, V}, title = {{Neutrophil Extracellular Traps Kill Bacteria}}, journal = {Science}, year = {2004}, volume = {303}, number = {5663}, pages = {1532--1535}, month = mar } @article{Laganowsky:2014ki, author = {Laganowsky, Arthur and Reading, Eamonn and Allison, Timothy M and Ulmschneider, Martin B and Degiacomi, Matteo T and Baldwin, Andrew J and Robinson, Carol V}, title = {{Membrane proteins bind lipids selectively to modulate their structure and function}}, journal = {Nature}, year = {2014}, volume = {510}, number = {7503}, pages = {172--175}, month = jun } @article{Fischer:2004ee, author = {Fischer, Hannes and Polikarpov, Igor and Craievich, Aldo F}, title = {{Average protein density is a molecular-weight-dependent function}}, journal = {Protein Sci.}, year = {2004}, volume = {13}, number = {10}, pages = {2825--2828} } @article{Amadei:1999wn, author = {Amadei, Andrea and Ceruso, Marc A. and Di Nola, Alfredo}, title = {{On the convergence of the conformational coordinates basis set obtained by the essential dynamics analysis of proteins' molecular dynamics simulations}}, journal = {Proteins: Struct., Funct., Bioinf.}, year = {1999}, volume = {36}, number = {4}, pages = {419--424} } @article{Fadeel:2009ei, author = {Fadeel, Bengt and Xue, Ding}, title = {{The ins and outs of phospholipid asymmetry in the plasma membrane: roles in health and disease}}, journal = {Critical Reviews in Biochemistry and Molecular Biology}, year = {2009}, volume = {44}, number = {5}, pages = {264--277}, month = oct } @article{Noinaj:2012jr, author = {Noinaj, Nicholas and Easley, Nicole C and Oke, Muse and Mizuno, Naoko and Gumbart, James and Boura, Evzen and Steere, Ashley N and Zak, Olga and Aisen, Philip and Tajkhorshid, Emad and Evans, Robert W and Gorringe, Andrew R and Mason, Anne B and Steven, Alasdair C and Buchanan, Susan K}, title = {{Structural basis for iron piracy by pathogenic Neisseria}}, journal = {Nature}, year = {2012}, volume = {483}, number = {7387}, pages = {53--58}, month = mar } @article{DeSimone:2014cb, author = {De Simone, Alfonso and Mote, Kaustubh R and Veglia, Gianluigi}, title = {{Structural Dynamics and Conformational Equilibria of SERCA Regulatory Proteins in Membranes by Solid-State NMR Restrained Simulations}}, journal = {Biophys. J.}, year = {2014}, volume = {106}, number = {12}, pages = {2566--2576}, month = jun } @article{Hilser:2007je, author = {Hilser, V J and Thompson, E B}, title = {{Intrinsic disorder as a mechanism to optimize allosteric coupling in proteins}}, journal = {Proc. Natl. Acad. Sci. U. S. A.}, year = {2007}, volume = {104}, number = {20}, pages = {8311--8315}, month = may } @article{Shlomovitz:2014kq, author = {Shlomovitz, Roie and Maibaum, Lutz and Schick, M}, title = {{Macroscopic Phase Separation, Modulated Phases, and Microemulsions: A Unified Picture of Rafts}}, journal = {Biophys. J.}, year = {2014}, volume = {106}, number = {9}, pages = {1979--1985}, month = may } @article{Beltrao:2007eb, author = {Beltrao, Pedro and Kiel, Christina and Serrano, Luis}, title = {{Structures in systems biology}}, journal = {Current Opinion in Structural Biology}, year = {2007}, volume = {17}, number = {3}, pages = {378--384} } @article{Zaccai:2011fr, author = {Zaccai, Giuseppe}, title = {{Neutron scattering perspectives for protein dynamics}}, journal = {J Non-Cryst Solids}, year = {2011}, volume = {357}, number = {2}, pages = {615--621} } @article{Musiani:2014bg, author = {Musiani, Francesco and Rossetti, Giulia and Capece, Luciana and Gerger, Thomas Martin and Micheletti, Cristian and Varani, Gabriele and Carloni, Paolo}, title = {{Molecular Dynamics Simulations Identify Time Scale of Conformational Changes Responsible for Conformational Selection in Molecular Recognition of HIV-1 Transactivation Responsive RNA}}, journal = {JACS}, year = {2014}, volume = {136}, number = {44}, pages = {15631--15637}, month = nov } @article{Habeck:2005vp, author = {Habeck, M and Nilges, M and Rieping, W}, title = {{Replica-exchange Monte Carlo scheme for Bayesian data analysis}}, journal = {Phys. Rev. Lett.}, year = {2005} } @article{Haselton:2003vy, author = {Haselton, Martie G and Buss, David M}, title = {{Biases in Social Judgment - Design Flaws or Design Features?}}, year = {2003}, pages = {1--23}, month = feb } @article{Rojas:2007wf, author = {Rojas, Ra{\'u}l}, title = {{Neural networks - a systematic introduction}}, year = {2007}, pages = {1--509}, month = mar } @article{Tietjen:2014bl, author = {Tietjen, Gregory T and Gong, Zhiliang and Chen, Chiu-Hao and Vargas, Ernesto and Crooks, James E and Cao, Kathleen D and Heffern, Charles T R and Henderson, J Michael and Meron, Mati and Lin, Binhua and Roux, Beno{\^\i}t and Schlossman, Mark L and Steck, Theodore L and Lee, Ka Yee C and Adams, Erin J}, title = {{Molecular mechanism for differential recognition of membrane phosphatidylserine by the immune regulatory receptor Tim4}}, journal = {Proc. Natl. Acad. Sci. U. S. A.}, year = {2014}, volume = {111}, number = {15}, pages = {E1463--E1472}, month = apr } @webpage{Anonymous:eFDlrxBG, title = {{Phys. Rev. Lett. 113, 225701 (2014) - Role of Structure and Entropy in Determining Differences in Dynamics for Glass Formers with Different Interaction Potentials}}, url = {http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.113.225701} } @article{Fukunaga:1969dw, author = {Fukunaga, K and Krile, T F}, title = {{Calculation of Bayes' Recognition Error for Two Multivariate Gaussian Distributions}}, journal = {IEEE Trans. Comput.}, year = {1969}, volume = {C-18}, number = {3}, pages = {220--229}, month = mar } @article{SMAdmin:2013uu, author = {{SMAdmin}}, title = {{Sensor Measurements NMEA Protocol}}, year = {2013}, pages = {1--24}, month = aug } @webpage{Anonymous:ROy-Bo2n, title = {{PLOS Computational Biology: A Unified View of {\textquotedblleft}How Allostery Works{\textquotedblright}}}, url = {http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003394} } @article{Saven:2011fa, author = {Saven, Jeffery G}, title = {{Computational protein design: engineering molecular diversity, nonnatural enzymes, nonbiological cofactor complexes, and membrane proteins}}, journal = {Current Opinion in Chemical Biology}, year = {2011}, volume = {15}, number = {3}, pages = {452--457}, month = jun } @article{Hinsen:2012ww, author = {Hinsen, Konrad}, title = {{Managing State}}, journal = {Computing in Science {\&} Engineering}, year = {2012}, volume = {14}, number = {1}, pages = {80--85} } @webpage{Owsinski:fgafby87, author = {Owsinski, Bibby}, title = {{The recording engineer's handbook}}, url = {http://audiodigitalymidi.pbworks.com/w/file/fetch/44088225/The%2520Recording%2520Engineer%2527s%2520Handbook%25202nd%2520ed%2520-%2520B.%2520Owsinski%2520%25282009%2529%2520159863867X.pdf} } @article{Konagurthu:2008hw, author = {Konagurthu, Arun S and Lesk, Arthur M.}, title = {{On the origin of distribution patterns of motifs in biological networks}}, journal = {BMC Syst Biol}, year = {2008}, volume = {2}, number = {1}, pages = {73} } @article{Gabdoulline:1997ua, author = {Gabdoulline, RR and Wade, RC}, title = {{Simulation of the diffusional association of Barnase and Barstar}}, journal = {Biophys. J.}, year = {1997}, volume = {72}, number = {5}, pages = {1917--1929} } @article{Karczmarczuk:1999wx, author = {Karczmarczuk, J}, title = {{Scientific computation and functional programming}}, journal = {Computing in Science {\&} Engineering}, year = {1999}, volume = {1}, number = {3}, pages = {64--72} } @article{Daniel:2003bp, author = {Daniel, RM and Dunn, RV and Finney, JL and Smith, JC}, title = {{The role of dynamics in enzyme activity}}, journal = {Annu Rev Bioph Biom}, year = {2003}, volume = {32}, pages = {69--92} } @article{Ghysels:2012wu, author = {Ghysels, An and Miller, Benjamin T and Pickard IV, Frank C and Brooks, Bernard R}, title = {{Comparing normal modes across different models and scales: Hessian reduction versus coarse-graining - Ghysels - 2012 - Journal of Computational Chemistry - Wiley Online Library}}, journal = {J. Comput. Chem.}, year = {2012}, volume = {33}, number = {28}, pages = {2250--2275}, month = sep } @article{Ota:2005wo, author = {Ota, N and Agard, DA}, title = {{Intramolecular signaling pathways revealed by modeling anisotropic thermal diffusion}}, journal = {J. Mol. Biol.}, year = {2005}, volume = {351}, number = {2}, pages = {345--354} } @article{Stansfeld:2011jc, author = {Stansfeld, Phillip J and Sansom, Mark S P}, title = {{Molecular Simulation Approaches to Membrane Proteins}}, journal = {Structure}, year = {2011}, volume = {19}, number = {11}, pages = {1562--1572}, month = nov } @article{PascualGarcia:2009bo, author = {Pascual-Garc{\'\i}a, Alberto and Abia, David and M{\'e}ndez, Raul and Nido, Gonzalo S and Bastolla, Ugo}, title = {{Quantifying the evolutionary divergence of protein structures: The role of function change and function conservation}}, journal = {Proteins: Struct., Funct., Bioinf.}, year = {2009}, pages = {NA--NA} } @article{Kneller:2008eb, author = {Kneller, Gerald R}, title = {{Eckart axis conditions, Gauss' principle of least constraint, and the optimal superposition of molecular structures}}, journal = {J. Chem. Phys.}, year = {2008}, volume = {128}, number = {19}, pages = {--} } @article{Munz:2010iz, author = {M{\"u}nz, M{\'a}rton and Lyngs{\o}, Rune and Hein, Jotun and Biggin, Philip C}, title = {{Dynamics based alignment of proteins: an alternative approach to quantify dynamic similarity.}}, journal = {BMC Bioinformatics}, year = {2010}, volume = {11}, pages = {188} } @article{Huse:1997wm, author = {Huse, G and Gjosaeter, H}, title = {{Fecundity of the Barents Sea capelin (Mallotus villosus)}}, journal = {Marine Biology}, year = {1997}, volume = {130}, number = {2}, pages = {309--313}, month = dec } @article{Shakhnovich:1996er, author = {Shakhnovich, E}, title = {{Modelling protein folding: the beauty and power of simplicity}}, journal = {Folding Des.}, year = {1996}, volume = {1}, number = {3}, pages = {R50--R54}, month = jun } @article{Kadamur:2013cf, author = {Kadamur, Ganesh and Ross, Elliott M}, title = {{Mammalian Phospholipase C}}, journal = {Annu. Rev. Physiol.}, year = {2013}, volume = {75}, number = {1}, pages = {127--154}, month = feb } @article{Perez:2005jb, author = {Perez, A and Blas, JR and Rueda, M and Lopez-Bes, JM and de la Cruz, X and Orozco, M}, title = {{Exploring the essential dynamics of B-DNA}}, journal = {J Chem Theory Comput}, year = {2005}, volume = {1}, number = {5}, pages = {790--800} } @article{Anonymous:253U5_gy, author = {Kim, Moon K and Chirikjian, Gregory S and Jernigan, Robert L}, title = {{Elastic models of conformational transitions in macromolecules.}}, journal = {Journal of Molecular Graphics and Modelling}, year = {2002}, volume = {21}, number = {2}, pages = {151--160}, month = oct } @article{Zallen:1985kf, author = {Zallen, Richard}, title = {{Models of amorphous solids}}, journal = {J Non-Cryst Solids}, year = {1985}, volume = {75}, number = {1-3}, pages = {3--14}, month = oct } @article{Oldham:2005fb, author = {Oldham, Michael L and Brash, Alan R and Newcomer, Marcia E}, title = {{Insights from the X-ray crystal structure of coral 8R-lipoxygenase: calcium activation via a C2-like domain and a structural basis of product chirality.}}, journal = {J. Biol. Chem.}, year = {2005}, volume = {280}, number = {47}, pages = {39545--39552}, month = nov } @article{Goethe:2014hi, author = {Goethe, Martin and Fita, Ignacio and Rubi, J Miguel}, title = {{Vibrational Entropy of a Protein: Large Differences between Distinct Conformations}}, journal = {J Chem Theory Comput}, year = {2014}, pages = {141201173501007}, month = dec } @article{Hess:2000tq, author = {Hess, B}, title = {{Similarities between principal components of protein dynamics and random diffusion}}, journal = {Phys. Rev. E}, year = {2000} } @article{Kuchaiev:2009uj, author = {Kuchaiev, O and Milenkovic, T and Memisevic, V and Hayes, W and Przulj, N}, title = {{Topological network alignment uncovers biological function and phylogeny}}, year = {2009} } @article{Potti:2007ba, title = {{Reply to 'Microarrays: retracing steps'}}, journal = {Nature Medicine}, year = {2007}, volume = {13}, number = {11}, pages = {1277}, month = nov } @article{Edgar:2004bo, author = {Edgar, R C}, title = {{MUSCLE: multiple sequence alignment with high accuracy and high throughput}}, journal = {Nucleic Acids Res.}, year = {2004}, volume = {32}, number = {5}, pages = {1792--1797}, month = mar } @article{Giardine:2005ig, author = {Giardine, Belinda and Riemer, Cathy and Hardison, Ross C and Burhans, Richard and Elnitski, Laura and Shah, Prachi and Zhang, Yi and Blankenberg, Daniel and Albert, Istvan and Taylor, James and Miller, Webb and Kent, W James and Nekrutenko, Anton}, title = {{Galaxy: a platform for interactive large-scale genome analysis.}}, journal = {Genome Res}, year = {2005}, volume = {15}, number = {10}, pages = {1451--1455}, month = oct } @article{Skeel:2009iw, author = {Skeel, Robert D}, title = {{What Makes Molecular Dynamics Work?}}, journal = {SIAM J. Sci. Comput.}, year = {2009}, volume = {31}, number = {2}, pages = {1363--1378}, month = jan } @article{Anishkin:to, author = {Anishkin, Andriy and Loukin, Stephen H and Teng, Jinfeng and Kung, Ching}, title = {{Feeling the hidden mechanical forces in lipid bilayer is an original sense}}, journal = {pnas.org} } @article{Gautier:2008iy, author = {Gautier, R and Douguet, D and Antonny, B and Drin, G}, title = {{HELIQUEST: a web server to screen sequences with specific ~-helical properties}}, journal = {Bioinformatics}, year = {2008}, volume = {24}, number = {18}, pages = {2101--2102}, month = sep } @article{Murakami:2011bn, author = {Murakami, Makoto and Taketomi, Yoshitaka and Sato, Hiroyasu and Yamamoto, Kei}, title = {{Secreted phospholipase A2 revisited.}}, journal = {J. Biochem.}, year = {2011}, volume = {150}, number = {3}, pages = {233--255}, month = sep } @article{Ford:2002if, author = {Ford, Marijn G J and Mills, Ian G and Peter, Brian J and Vallis, Yvonne and Praefcke, Gerrit J K and Evans, Philip R and McMahon, Harvey T}, title = {{Curvature of clathrin-coated pits driven by epsin.}}, journal = {Nature}, year = {2002}, volume = {419}, number = {6905}, pages = {361--366}, month = sep } @article{Ascher:2001ty, author = {Ascher, D and Dubois, P F and Hinsen, K and Hugunin, J and Oliphant, T}, title = {{Numerical python}}, year = {2001} } @article{Tiwari:2014cbb, author = {Tiwari, Sandhya P and Fuglebakk, Edvin and Hollup, Siv M and Skjaerven, Lars and Cragnolini, Tristan and Grindhaug, Svenn H and Tekle, Kidane M and Reuter, Nathalie}, title = {{WEBnm@ v2.0: Web server and services for comparing protein flexibility.}}, journal = {BMC Bioinformatics}, year = {2014}, volume = {15}, number = {1}, pages = {6597}, month = dec } @article{Helmstaedt:2001dq, author = {Helmstaedt, K and Krappmann, S and Braus, G H}, title = {{Allosteric Regulation of Catalytic Activity: Escherichia coli Aspartate Transcarbamoylase versus Yeast Chorismate Mutase}}, journal = {Microbiology and molecular biology reviews}, year = {2001}, volume = {65}, number = {3}, pages = {404--421}, month = sep } @article{Clifford:2005wx, author = {Clifford, David}, title = {{Computation of Spatial Covariance Matrices}}, journal = {Journal of Computational and Graphical Statistics}, year = {2005}, volume = {14}, number = {1}, pages = {155--167}, month = mar } @article{Drucker:2014cs, author = {Dr{\"u}cker, Patrick and Pejic, Milena and Grill, David and Galla, Hans-Joachim and Gerke, Volker}, title = {{Cooperative Binding of Annexin A2 to Cholesterol- and Phosphatidylinositol-4,5-Bisphosphate-Containing Bilayers}}, journal = {Biophys. J.}, year = {2014}, volume = {107}, number = {9}, pages = {2070--2081}, month = nov } @article{Singh:2014vh, author = {Singh, Harkewal and Arentson, Benjamin W and Becker, Donald F and Tanner, John J}, title = {{Structures of the PutA peripheral membrane flavoenzyme reveal a dynamic substrate-channeling tunnel and the quinone-binding site}}, journal = {Proceedings of the {\ldots}}, year = {2014} } @article{Liberles:2012ir, author = {Liberles, David A and Teichmann, Sarah A and Bahar, Ivet and Bastolla, Ugo and Bloom, Jesse and Bornberg-Bauer, Erich and Colwell, Lucy J and de Koning, A P Jason and Dokholyan, Nikolay V and Echave, Juli{\'a}n and Elofsson, Arne and Gerloff, Dietlind L and Goldstein, Richard A and Grahnen, Johan A and Holder, Mark T and Lakner, Clemens and Lartillot, Nicholas and Lovell, Simon C and Naylor, Gavin and Perica, Tina and Pollock, David D and Pupko, Tal and Regan, Lynne and Roger, Andrew and Rubinstein, Nimrod and Shakhnovich, Eugene and Sj{\"o}lander, Kimmen and Sunyaev, Shamil and Teufel, Ashley I and Thorne, Jeffrey L and Thornton, Joseph W and Weinreich, Daniel M and Whelan, Simon}, title = {{The interface of protein structure, protein biophysics, and molecular evolution.}}, journal = {Protein Sci.}, year = {2012}, volume = {21}, number = {6}, pages = {769--785}, month = jun } @article{Moravcevic:2015iu, author = {Moravcevic, Katarina and Alvarado, Diego and Schmitz, Karl R and Kenniston, Jon A and Mendrola, Jeannine M and Ferguson, Kathryn M and Lemmon, Mark A}, title = {{Comparison of Saccharomyces cerevisiae F-BAR Domain Structures Reveals a Conserved Inositol Phosphate Binding Site}}, journal = {Structure}, year = {2015}, volume = {23}, number = {2}, pages = {352--363}, month = feb } @article{Mori:2006gp, author = {Mori, Kazuki and Seki, Yasutaka and Yamada, Yutaka and Matsumoto, Hiroki and Soda, Kunitsugu}, title = {{Evaluation of intrinsic compressibility of proteins by molecular dynamics simulation}}, journal = {J. Chem. Phys.}, year = {2006}, volume = {125}, number = {5}, pages = {054903} } @article{Dodson:2006ka, author = {Dodson, G and Verma, CS}, title = {{Protein flexibility: its role in structure and mechanism revealed by molecular simulations}}, journal = {Cell Mol Life Sci}, year = {2006}, volume = {63}, number = {2}, pages = {207--219} } @webpage{Anonymous:7_0gqDWt, title = {{biochemistry10.pdf}}, url = {http://www.uu.nl/SiteCollectionDocuments/Beta/Medicinal%20Chemistry/biochemistry10.pdf} } @article{Hinsen:2014ho, author = {Hinsen, Konrad}, title = {{Platforms for publishing and archiving computer-aided~research}}, journal = {F1000Res}, year = {2014}, month = nov } @webpage{Anonymous:1DzqaDbB, title = {{On the relationship between low-frequency normal modes and the large-scale conformational changes of proteins}}, url = {http://www.sciencedirect.com/science/article/pii/S0003986114004457} } @article{Kneller:2014ui, author = {Kneller, Gerald R and Hinsen, Konrad}, title = {{Protein secondary structure analysis with a coarse-grained model}}, journal = {arXiv}, year = {2014}, eprint = {1412.8202v1}, eprinttype = {arxiv}, eprintclass = {q-bio.BM}, month = dec } @article{BCampos:1998fa, author = {{B Campos} and {Y D Mo} and {T R Mealy} and {C W Li} and {M A Swairjo} and {C Balch} and {J F Head} and {G Retzinger} and J R Dedman, and and {B A Seaton}}, title = {{Mutational and Crystallographic Analyses of Interfacial Residues in Annexin V Suggest Direct Interactions with Phospholipid Membrane Components{\dag},{\ddag}}}, journal = {Biochemistry}, year = {1998}, volume = {37}, number = {22}, pages = {8004--8010}, month = jun } @article{Pandini:2007bqa, author = {Pandini, Alessandro and Mauri, Giancarlo and Bordogna, Annalisa and Bonati, Laura}, title = {{Supplementary Material: Detecting similarities among distant homologous proteins by comparison of domain flexibilities}}, journal = {Protein Eng Des Sel}, year = {2007}, volume = {20}, number = {6}, pages = {285--299} } @article{Hinsen:2000kn, author = {Hinsen, Konrad and Kneller, Gerald}, title = {{Projection Methods for the Analysis of Complex Motions in Macromolecules}}, journal = {Mol. Simulation}, year = {2000}, volume = {23}, number = {4}, pages = {275--292}, month = mar } @article{Herrera:tt, author = {Herrera, Guillermo E and Moeller, Holly V and Neubert, Michael G}, title = {{High-seas fish wars generate marine reserves}}, journal = {pnas.org} } @article{Nicolay:2006fm, author = {Nicolay, S and Sanejouand, Y-H}, title = {{Functional Modes of Proteins Are among the Most Robust}}, journal = {Phys. Rev. Lett.}, year = {2006}, volume = {96}, number = {7}, pages = {4}, month = feb } @article{HenzlerWildman:2007jb, author = {Henzler-Wildman, Katherine and Kern, Dorothee}, title = {{Dynamic personalities of proteins}}, journal = {Nature}, year = {2007}, volume = {450}, number = {7172}, pages = {964--972} } @article{Micheletti:1999vz, author = {Micheletti, C and Banavar, JR and Maritan, A and Seno, F}, title = {{Protein structures and optimal folding from a geometrical variational principle}}, journal = {Phys. Rev. Lett.}, year = {1999}, volume = {82}, number = {16}, pages = {3372--3375} } @book{Petsko:2004wf, author = {Petsko, G and Ringe, D}, title = {{Protein Structure and Function}}, publisher = {New Science Press}, year = {2004} } @webpage{AbouMoustafa:wo, author = {Abou-Moustafa, Karim T and De La Torre, Fernando and Ferrie, Frank P}, title = {{Designing a Metric for the Difference Between Gaussian Densities}}, url = {http://www.andrew.cmu.edu/user/karimt/KAM_AISC2010.pdf} } @article{Kondrashov:2007eh, author = {Kondrashov, Dmitry A and Van Wynsberghe, Adam W and Bannen, Ryan M and Cui, Qiang and Phillips, George N}, title = {{ScienceDirect.com - Structure - Protein Structural Variation in Computational Models and Crystallographic Data}}, journal = {Structure}, year = {2007}, volume = {15}, number = {2}, pages = {169--177} } @article{Hadley:1999wu, author = {Hadley, C and Jones, DT}, title = {{A systematic comparison of protein structure classifications: SCOP, CATH and FSSP}}, journal = {Structure}, year = {1999}, volume = {7}, number = {9}, pages = {1099--1112} } @article{Daleke:2003te, author = {Daleke, David L}, title = {{Regulation of transbilayer plasma membrane phospholipid asymmetry}}, year = {2003} } @article{Sun:2014fh, author = {Sun, Yen and Sun, Tzu-Lin and Huang, Huey W}, title = {{Physical Properties of Escherichia coli Spheroplast Membranes}}, journal = {Biophys. J.}, year = {2014}, volume = {107}, number = {9}, pages = {2082--2090}, month = nov } @article{AGLEN:2003tn, author = {AGLEN, Asgeir 1994}, title = {{Chapter 7 Sources of Error in Acoustic Estimation of Fish Abundance}}, year = {2003}, pages = {1--29}, month = feb } @article{Graves:2011uv, author = {Graves, LiLynn}, title = {{Scientific Poster Design}}, year = {2011}, pages = {1--68}, month = sep } @article{Sanderson:2007ie, author = {Sanderson, John M}, title = {{Refined models for the preferential interactions of tryptophan with phosphocholines}}, journal = {Org. Biomol. Chem.}, year = {2007}, volume = {5}, number = {20}, pages = {3276} } @article{Shi:wf, author = {Shi, Xuesong and Beauchamp, Kyle A and Harbury, Pehr B and Herschlag, Daniel}, title = {{From a structural average to the conformational ensemble of a DNA bulge}}, journal = {pnas.org} } @article{Liu:2012tr, author = {Liu, L. and Gronenborn, A.M. and Bahar, I}, title = {{Longer simulations sample larger subspaces of conformations while maintaining robust mechanisms of motion}}, journal = {Proteins: Struct., Funct., Bioinf.}, year = {2012}, volume = {80}, number = {2}, pages = {616--625} } @article{Muller:1996dc, author = {M{\"u}ller, C W and Schlauderer, G J and Reinstein, J and Schulz, G E}, title = {{Adenylate kinase motions during catalysis: an energetic counterweight balancing substrate binding}}, journal = {Structure}, year = {1996}, volume = {4}, number = {2}, pages = {147--156}, month = feb } @article{Roux:2007fj, author = {Roux, B}, title = {{Lonely Arginine Seeks Friendly Environment}}, journal = {The Journal of General Physiology}, year = {2007}, volume = {130}, number = {2}, pages = {233--236}, month = jul } @article{Frstner:2000vf, author = {Frstner, Wolfgang and Moonen, Boudewijn and Gauss, Carl Friedrich}, title = {{A Metric for Covariance Matrices}}, year = {2000}, month = jan } @article{Uversky:2013dp, author = {Uversky, Vladimir N}, title = {{Unusual biophysics of intrinsically disordered proteins.}}, journal = {Biochim. Biophys. Acta}, year = {2013}, volume = {1834}, number = {5}, pages = {932--951}, month = may } @article{Spiwok:2007ji, author = {Spiwok, Vojtech and Lipovova, Petra and Kralova, Blanka}, title = {{Metadynamics in Essential Coordinates:~ Free Energy Simulation of Conformational Changes}}, journal = {J. Phys. Chem. B}, year = {2007}, volume = {111}, number = {12}, pages = {3073--3076}, month = mar } @article{Zhang:2014eo, author = {Zhang, H and Kurgan, L}, title = {{Sequence-based Gaussian network model for protein dynamics}}, journal = {Bioinformatics}, year = {2014}, volume = {30}, number = {4}, pages = {497--505}, month = feb } @article{Hub:2009ga, author = {Hub, Jochen S and de Groot, Bert L}, title = {{Detection of functional modes in protein dynamics.}}, journal = {PLoS Comput. Biol.}, year = {2009}, volume = {5}, number = {8}, pages = {e1000480}, month = aug } @article{Sondre:2003gg, author = {Sondre, Aanes and Pennington, Michael}, title = {{On estimating the age composition of the commercial catch of Northeast Arctic cod from a sample of clusters}}, journal = {ICES J. Mar. Sci.}, year = {2003}, volume = {60}, number = {2}, pages = {297--303}, month = jan } @article{BenTal:2000fk, author = {Ben-Tal, Nir and Honig, Barry and Bagdassarian, Carey K and Ben-Shaul, Avinoam}, title = {{Association Entropy in Adsorption Processes}}, journal = {Biophys. J.}, year = {2000}, volume = {79}, number = {3}, pages = {1180--1187}, month = sep } @article{Holbrook:2008ik, author = {Holbrook, Stephen R}, title = {{Structural Principles From Large RNAs *}}, journal = {Annu. Rev. Biophys.}, year = {2008}, volume = {37}, number = {1}, pages = {445--464}, month = jun } @article{Jahnig:1976hd, author = {J{\"a}hnig, Fritz}, title = {{Electrostatic free energy and shift of the phase transition for charged lipid membranes}}, journal = {Biophys. Chem.}, year = {1976}, volume = {4}, number = {4}, pages = {309--318}, month = jul } @article{Petersen:te, author = {Petersen, Alexander Michael and Fortunato, Santo and Pan, Raj K and Kaski, Kimmo and Penner, Orion and Rungi, Armando and Riccaboni, Massimo and Stanley, H Eugene and Pammolli, Fabio}, title = {{Reputation and impact in academic careers}}, journal = {pnas.org} } @article{Yasui:2014ey, author = {Yasui, Masato and Matsuoka, Satomi and Ueda, Masahiro}, title = {{PTEN Hopping on the Cell Membrane Is Regulated via a Positively-Charged C2 Domain.}}, journal = {PLoS Comput. Biol.}, year = {2014}, volume = {10}, number = {9}, pages = {e1003817}, month = sep } @article{Zaccai:2000gt, author = {Zaccai, G}, title = {{How Soft Is a Protein? A Protein Dynamics Force Constant Measured by Neutron Scattering}}, journal = {Science}, year = {2000}, volume = {288}, number = {5471}, pages = {1604--1607}, month = jun } @article{Anonymous:n-75ICyP, title = {{Kvantemekanikk - kompendie 3 - 6}}, year = {2005}, pages = {1--81}, month = oct } @article{Granseth:2005tm, author = {Granseth, E and von Heijne, G and Elofsson, A}, title = {{ScienceDirect.com - Journal of Molecular Biology - A Study of the Membrane{\textendash}Water Interface Region of Membrane Proteins}}, journal = {J. Mol. Biol.}, year = {2005} } @article{Axler:2009wr, author = {Axler, Sheldon}, title = {{Down with Determinats!}}, year = {2009}, pages = {1--18}, month = feb } @article{Pandini:2007bq, author = {Pandini, Alessandro and Mauri, Giancarlo and Bordogna, Annalisa and Bonati, Laura}, title = {{Detecting similarities among distant homologous proteins by comparison of domain flexibilities}}, journal = {Protein Enginering Design {\&} Selection}, year = {2007}, volume = {20}, number = {6}, pages = {285--299}, month = jun } @article{Kobayashi:1997jw, author = {Kobayashi, Nobuo and Yamato, Takahisa and Go, Nobuhiro}, title = {{Mechanical property of a TIM-barrel protein}}, journal = {Proteins: Struct., Funct., Bioinf.}, year = {1997}, volume = {28}, number = {1}, pages = {109--116}, month = may } @article{Clark:2015jb, author = {Clark, Alex M and Dole, Krishna and Coulon-Spektor, Anna and McNutt, Andrew and Grass, George and Freundlich, Joel S and Reynolds, Robert C and Ekins, Sean}, title = {{Open Source Bayesian Models. 1. Application to ADME/Tox and Drug Discovery Datasets}}, journal = {J Chem Inf Model}, year = {2015}, volume = {55}, number = {6}, pages = {1231--1245}, month = jun } @article{Escriba:tw, author = {Escrib{\'a}, P V and Ozaita, A and Ribas, C and Miralles, A and Fodor, E and Farkas, T and Garc{\'\i}a-Sevilla, J A}, title = {{Role of lipid polymorphism in G protein-membrane interactions: nonlamellar-prone phospholipids and peripheral protein binding to membranes.}}, journal = {Proc Natl Acad Sci U S A}, year = {1997}, volume = {94}, number = {21}, pages = {11375--11380}, month = oct } @webpage{Shewchuk:1994uc, author = {Shewchuk, Jonathan Richard}, title = {{An Introduction to the Conjugate Gradient Method Without the Agonizing Pain}}, year = {1994}, month = aug, url = {http://www.cs.cmu.edu/~quake-papers/painless-conjugate-gradient.pdf} } @article{Wilmot:1988vb, author = {Wilmot, C M and Thornton, J M}, title = {{Analysis and prediction of the different types of $\beta$-turn in proteins}}, journal = {J. Mol. Biol.}, year = {1988}, volume = {203}, number = {1}, pages = {221--232}, month = sep } @incollection{Kessel:2002ft, author = {Kessel, Amit and Ben-Tal, Nir}, title = {{Free energy determinants of peptide association with lipid bilayers}}, booktitle = {Current topics in membranes}, year = {2002}, pages = {205--253}, publisher = {Elsevier} } @article{Cuchillo:2015bp, author = {Cuchillo, Remi and Pinto-Gil, Kevin and Michel, Julien}, title = {{A Collective Variable for the Rapid Exploration of Protein Druggability}}, journal = {J Chem Theory Comput}, year = {2015}, pages = {150122122603000}, month = jan } @article{Skaug:2016kj, author = {Skaug, Eli-Anne and Nes, Bjarne and Aspenes, Stian Thoresen and Ellingsen, {\O}yvind}, title = {{Non-Smoking Tobacco Affects Endothelial Function in Healthy Men in One of the Largest Health Studies Ever Performed; The Nord-Tr{\o}ndelag Health Study in Norway; HUNT3}}, journal = {PLoS ONE}, year = {2016}, volume = {11}, number = {8}, pages = {e0160205}, month = aug } @webpage{Anonymous:HU-zaoMG, title = {{PLOS Computational Biology: Sensing Membrane Stresses by Protein Insertions}}, url = {http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003556} } @webpage{Anonymous:kceNrBQS, title = {{Estimating environmental preferences of South African pelagic fish species using catch size- and remote sensing data}}, url = {http://www.sciencedirect.com/science/article/pii/S0079661103001708} } @article{Huse:1999ww, author = {Huse, G and Gjosaeter, H}, title = {{A neural network approach for predicting stock abundance of the Barents Sea capelin}}, journal = {Sarsia}, year = {1999}, volume = {84}, number = {5-6}, pages = {457--464} } @article{BURGES:1998wd, author = {BURGES, CHRISTOPHER JC}, title = {{A Tutorial on Support Vector Machines for Pattern Recognition}}, year = {1998}, pages = {1--47}, month = oct } @article{Mathias:2009bj, author = {Mathias, Jordan D and Ran, Yong and Carter, Jeffery D and Fanucci, Gail E}, title = {{Interactions of the GM2 Activator Protein with Phosphatidylcholine Bilayers: A Site-Directed Spin-Labeling Power Saturation Study}}, journal = {Biophys. J.}, year = {2009}, volume = {97}, number = {5}, pages = {1436--1444}, month = sep } @article{Anonymous:Ujb3NX9U, author = {Bogstad, B and Tjelmeland, S and Subbey, S}, title = {{A retrospective evaluation of the Barents Sea capelin management advice}}, journal = {Marine Biology}, year = {2015}, volume = {11}, number = {2}, pages = {135--143} } @article{Marzban:2004vs, author = {Marzban, Caren}, title = {{A Comment on the ROC Curve and the Area Under it as Performance Measures}}, year = {2004}, pages = {1--26}, month = jun } @article{Kleinjung:2004fh, author = {Kleinjung, J}, title = {{Contact-based sequence alignment}}, journal = {Nucleic Acids Res.}, year = {2004}, volume = {32}, number = {8}, pages = {2464--2473}, month = apr } @article{Samuel:fn, author = {Samuel, Moore and Cameron, Neylon and Martin Paul, Eve and Daniel, O'Donnell and Damian, Pattinson}, title = {{Excellence R Us: University Research and the Fetishisation of Excellence}}, journal = {figshare.com} } @webpage{Anonymous:4DxEUNHk, title = {{Phys. Rev. Lett. 113, 228101 (2014) - Structure of Cholesterol in Lipid Rafts}}, url = {http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.113.228101} } @article{Martin:1998vg, author = {Martin, ACR and Orengo, CA and Hutchinson, EG and Jones, S and Karmirantzou, M and Laskowski, RA and Mitchell, JBO and Taroni, C and Thornton, JM}, title = {{Protein folds and functions}}, journal = {Structure}, year = {1998}, volume = {6}, number = {7}, pages = {875--884} } @article{Dehouck:2013ub, author = {Dehouck, Yves and Mikhailov, Alexander S}, title = {{preprint: Effective harmonic potentials: insights into the internal cooperativity and sequence-specificity of protein dynamics}}, journal = {arXiv}, year = {2013}, month = apr } @article{Hasegawa:1985ww, author = {Hasegawa, M and Kishino, H and Yano, T}, title = {{Dating of the human-ape splitting by a molecular clock of mitochondrial DNA}}, journal = {Journal of Molecular Evolution}, year = {1985}, volume = {22}, number = {2}, pages = {160--174} } @article{Anonymous:Fpn1PFRm, title = {{Electrostatic Enhancement of Diffusion-controlled Protein{\textpm}Protein Association: Comparison of Theory and Experiment on Barnase and Barstar}}, year = {1998}, pages = {1--10}, month = may } @article{Iyer:2014js, author = {Iyer, Aditya and Petersen, Nils O and Claessens, Mireille M A E and Subramaniam, Vinod}, title = {{Amyloids of Alpha-Synuclein Affect the Structure and Dynamics of Supported Lipid Bilayers}}, journal = {Biophys. J.}, year = {2014}, volume = {106}, number = {12}, pages = {2585--2594}, month = jun } @article{Ahmed:2010ci, author = {Ahmed, Aqeel and Villinger, Saskia and Gohlke, Holger}, title = {{Large-scale comparison of protein essential dynamics from molecular dynamics simulations and coarse-grained normal mode analyses}}, journal = {Proteins: Struct., Funct., Bioinf.}, year = {2010}, volume = {78}, number = {16}, pages = {3341--3352} } @article{Feynman:1974vr, author = {Feynman, Richard P}, title = {{Cargo Cult Science}}, year = {1974}, number = {Caltech's 1974 commencement address}, pages = {1--4} } @manual{Anonymous:bOROwpN6, title = {{Johnson - Evinrude Service Manual (65-300 Hp, 1992-2001)}}, month = jun, year = {2006} } @article{Darlington:1973tc, author = {Darlington, Richard and Weinberg, Sharon and Walberg, Herbert}, title = {{Canonical Variate Analysis and Related Techniques}}, journal = {Review of Educational Research}, year = {1973}, volume = {43}, number = {4}, pages = {433--454}, month = oct } @webpage{Anonymous:hANC6-p0, title = {{New insights into the meaning and usefulness of principal component analysis of concatenated trajectories - Pierdominici-Sottile - 2014 - Journal of Computational Chemistry - Wiley Online Library}}, url = {http://onlinelibrary.wiley.com/doi/10.1002/jcc.23811/full} } @article{schweiler:O71DFme_, author = {schweiler, RB}, title = {{Collective protein dynamics and nuclear spin relaxation}}, year = {1995}, pages = {8}, month = jun } @article{Atilgan:2001wd, author = {Atilgan, AR and Durell, SR and Jernigan, RL and Demirel, MC and Keskin, O and Bahar, I}, title = {{Anisotropy of fluctuation dynamics of proteins with an elastic network model}}, journal = {Biophys. J.}, year = {2001}, volume = {80}, number = {1}, pages = {505--515} } @article{Sun:2003cw, author = {Sun, Sean and Chandler, David and Dinner, Aaron R and Oster, George}, title = {{Elastic energy storage in ?-sheets with application to F1-ATPase}}, journal = {Eur Biophys J}, year = {2003}, volume = {32}, number = {8}, pages = {676--683}, month = dec } @article{Skjaerven:2011ec, author = {Skjaerven, Lars and Martinez, Aurora and Reuter, Nathalie}, title = {{Principal component and normal mode analysis of proteins; a quantitative comparison using the GroEL subunit.}}, journal = {Proteins: Struct., Funct., Bioinf.}, year = {2011}, volume = {79}, number = {1}, pages = {232--243}, month = jan } @article{Cheng:2013dq, author = {Cheng, Jiongjia and Karri, Sashank and Grauffel, Cedric and Wang, Fang and Reuter, Nathalie and Roberts, Mary F and Wintrode, Patrick L and Gershenson, Anne}, title = {{Does Changing the Predicted Dynamics of a Phospholipase C Alter Activityand Membrane Binding?}}, journal = {Biophysj}, year = {2013}, volume = {104}, number = {1}, pages = {185--195}, month = jan } @article{Giske:2011cua, author = {Giske, Jarl and Skjoldal, Hein Rune and Aksnes, Dag L}, title = {{A conceptual model of distribution of capelin in the Barents Sea}}, journal = {Sarsia}, year = {2011}, volume = {77}, number = {2}, pages = {147--156}, month = dec } @article{Tong:wq, author = {Tong, Jing and Sadreyev, Ruslan I and Pei, Jimin and Kinch, Lisa N and Grishin, Nick V}, title = {{Using homology relations within a database markedly boosts protein sequence similarity search}}, journal = {pnas.org} } @article{Franz:2010jt, author = {Franz, Mathias and Caillaud, Damien}, title = {{Fitting Artificial Neural Network Models to Animal Movement Data: Some Necessary Precautions, a Comment on Dalziel et al.}}, journal = {Am Nat}, year = {2010}, volume = {175}, number = {6}, pages = {759--761}, month = jun } @article{Scott:2006wn, author = {Scott, C and Brown, S and Ojha, S and Seffernick, J}, title = {{Leveraging Enzyme Structure{\textminus} Function Relationships for Functional Inference and Experimental Design: The Structure{\textminus} Function Linkage Database{\dag}}}, journal = {Biochemistry}, year = {2006} } @article{MarinoBuslje:2010vg, author = {Marino Buslje, C and Teppa, E and Di Dom{\'e}nico, T}, title = {{Networks of High Mutual Information Define the Structural Proximity of Catalytic Sites: Implications for Catalytic Residue Identification}}, journal = {PLoS Comput. Biol.}, year = {2010} } @article{Drubin:2011dl, author = {Drubin, David}, title = {{Any jackass can trash a manuscript, but it takes good scholarship to create one (how MBoC promotes civil and constructive peer review).}}, journal = {Mol. Biol. Cell}, year = {2011}, volume = {22}, number = {5}, pages = {3}, month = mar } @article{Morra:2012fh, author = {Morra, Giulia and Potestio, Raffaello and Micheletti, Cristian and Colombo, Giorgio}, title = {{Corresponding Functional Dynamics across the Hsp90 Chaperone Family: Insights from a Multiscale Analysis of MD Simulations}}, journal = {PLoS Comput. Biol.}, year = {2012}, volume = {8}, number = {3}, pages = {e1002433}, month = mar } @article{Gavish:2011hv, author = {Gavish, Matan and Donoho, David}, title = {{A Universal Identifier for Computational Results}}, journal = {Procedia Computer Science}, year = {2011}, volume = {4}, pages = {637--647}, month = jan } @article{Stahelin:2014hn, author = {Stahelin, Robert V and Scott, Jordan L and Frick, Cary T}, title = {{Cellular and molecular interactions of phosphoinositides and peripheral proteins}}, journal = {Chemistry and Physics of Lipids}, year = {2014}, volume = {182}, pages = {3--18}, month = sep } @article{Gruebele:2014fb, author = {Gruebele, Martin}, title = {{Protein Dynamics in Simulation and Experiment}}, journal = {JACS}, year = {2014}, volume = {136}, number = {48}, pages = {16695--16697}, month = dec } @article{Rueda:2007ju, author = {Rueda, Manuel and Chac{\'o}n, Pablo and Orozco, Modesto}, title = {{Thorough validation of protein normal mode analysis: a comparative study with essential dynamics}}, journal = {Structure}, year = {2007}, volume = {15}, number = {5}, pages = {565--575}, month = may } @article{Mitternacht:2011eq, author = {Mitternacht, Simon and Berezovsky, Igor N.}, title = {{A geometry-based generic predictor for catalytic and allosteric sites}}, journal = {Protein Eng Des Sel}, year = {2011}, volume = {24}, number = {4}, pages = {405--409} } @article{Ulmschneider:2001kg, author = {Ulmschneider, Martin B and Sansom, Mark S P}, title = {{Amino acid distributions in integral membrane protein structures}}, journal = {Biochimica et Biophysica Acta (BBA) - Biomembranes}, year = {2001}, volume = {1512}, number = {1}, pages = {1--14}, month = may } @article{Lezon:2010wo, author = {Lezon, T and Bahar, I}, title = {{Using Entropy Maximization to Understand the Determinants of Structural Dynamics beyond Native Contact Topology}}, journal = {ncbi.nlm.nih.gov}, year = {2010} } @article{Sevcsik:2011dc, author = {Sevcsik, Eva and Trexler, Adam J and Dunn, Joanna M and Rhoades, Elizabeth}, title = {{Allostery in a Disordered Protein: Oxidative Modifications to $\alpha$-Synuclein Act Distally To Regulate Membrane Binding}}, journal = {JACS}, year = {2011}, volume = {133}, number = {18}, pages = {7152--7158}, month = may } @webpage{Anonymous:EdCPDz3C, title = {{S0006-3495(14)01008-X.pdf}}, url = {http://www.cell.com/biophysj/pdf/S0006-3495(14)01008-X.pdf} } @article{Koontz:1972bn, author = {Koontz, W L G and Fukunaga, K}, title = {{A Nonlinear Feature Extraction Algorithm Using Distance Transformation}}, journal = {IEEE Trans. Comput.}, year = {1972}, volume = {C-21}, number = {1}, pages = {56--63} } @webpage{Anonymous:SmAC5eSP, title = {{Phys. Rev. Lett. 113, 148001 (2014) - Mechanical Characterization of Partially Crystallized Sphere Packings}}, url = {http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.113.148001} } @article{Pop:2015io, author = {Pop, Mihai and Salzberg, Steven L}, title = {{Use and mis-use of supplementary material in science publications}}, journal = {BMC Bioinformatics}, year = {2015}, volume = {16}, number = {1}, pages = {343}, month = nov } @article{Luebbering:2012is, author = {Luebbering, Emily K and Mick, Jacob and Singh, Ranjan K and Tanner, John J and Mehra-Chaudhary, Ritcha and Beamer, Lesa J}, title = {{Conservation of Functionally Important Global Motions in an Enzyme Superfamily across Varying Quaternary Structures}}, journal = {J. Mol. Biol.}, year = {2012}, volume = {423}, number = {5}, pages = {831--846}, month = nov } @article{Wiederstein:2014jq, author = {Wiederstein, Markus and Gruber, Markus and Frank, Karl and Melo, Francisco and Sippl, Manfred J}, title = {{Structure-Based Characterization of Multiprotein Complexes}}, journal = {Structure}, year = {2014}, volume = {22}, number = {7}, pages = {1063--1070}, month = jul } @article{Zhou:1997fc, author = {Zhou, H X}, title = {{Enhancement of protein-protein association rate by interaction potential: accuracy of prediction based on local Boltzmann factor}}, journal = {Biophys. J.}, year = {1997}, volume = {73}, number = {5}, pages = {2441--2445}, month = nov } @article{Jablin:2014cj, author = {Jablin, M S and Akabori, K and Nagle, J F}, title = {{Experimental Support for Tilt-Dependent Theory of Biomembrane Mechanics}}, journal = {Phys. Rev. Lett.}, year = {2014}, volume = {113}, number = {24}, pages = {248102}, month = dec } @article{Miyazawa:1985dh, author = {Miyazawa, Sanzo and Jernigan, Robert L}, title = {{Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation}}, journal = {Macromolecules}, year = {1985}, volume = {18}, number = {3}, pages = {534--552}, month = may } @article{Wako:2013hs, author = {Wako, Hiroshi and Endo, Shigeru}, title = {{Normal mode analysis based on an elastic network model for biomolecules in the Protein Data Bank, which uses dihedral angles as independent variables}}, journal = {Computational Biology and Chemistry}, year = {2013}, volume = {44}, pages = {22--30}, month = jun } @article{Good:2014bf, author = {Good, Daryl B and Wang, Shenlin and Ward, Meaghan E and Struppe, Jochem and Brown, Leonid S and Lewandowski, J{\'o}zef R and Ladizhansky, Vladimir}, title = {{Conformational Dynamics of a Seven Transmembrane Helical Protein Anabaena Sensory Rhodopsin Probed by Solid-State NMR}}, journal = {JACS}, year = {2014}, volume = {136}, number = {7}, pages = {2833--2842}, month = feb } @article{Dobbins:2008ch, author = {Dobbins, Sara E and Lesk, Victor I and Sternberg, Michael J E}, title = {{Insights into protein flexibility: The relationship between normal modes and conformational change upon protein-protein docking.}}, journal = {Proc. Natl. Acad. Sci. U. S. A.}, year = {2008}, volume = {105}, number = {30}, pages = {10390--10395}, month = jul } @article{Srivastava:2012ws, author = {Srivastava, Amit and Ben Halevi, Roee and Veksler, Alexander and Granek, Rony}, title = {{Tensorial elastic network model for protein dynamics: Integration of the anisotropic network model with bond-bending and twist elasticities}}, journal = {Proteins: Struct., Funct., Bioinf.}, year = {2012}, volume = {80}, number = {12}, pages = {2692--2700} } @article{Vaney:1996uv, author = {Vaney, M C and Maignan, S and Ries-Kautt, M and Ducruix, A}, title = {{High-resolution structure (1.33 angstrom) of a HEW lysozyme tetragonal crystal grown in the APCF apparatus. Data and structural comparison with a crystal grown under microgravity from SpaceHab-01 mission}}, journal = {Acta Crystallogr D}, year = {1996}, volume = {52}, pages = {505--517} } @article{Anonymous:Owp7e2k6, title = {{The norwegian reference fleeT}}, year = {2010}, pages = {1--12}, month = aug } @manual{Team:2008wf, title = {{\emph{R: A Language and Environment for Statistical Computing}}}, author = {Team, R Development Core}, organization = {R Foundation for Statistical Computing}, year = {2008} } @article{Leioatts:2012js, author = {Leioatts, Nicholas and Romo, Tod D. and Grossfield, Alan}, title = {{Elastic Network Models Are Robust to Variations in Formalism}}, journal = {J Chem Theory Comput}, year = {2012}, volume = {8}, number = {7}, pages = {2424--2434}, month = jun } @article{Zhou:1996id, author = {Zhou, Huan-Xiang}, title = {{Chemically Driven Motility of Brownian Particles}}, journal = {Phys. Rev. Lett.}, year = {1996}, volume = {77}, number = {1}, pages = {194--197}, month = jul } @article{Maunder:2015fi, author = {Maunder, Mark N and Piner, Kevin R}, title = {{Contemporary fisheries stock assessment: many issues still remain}}, journal = {ICES J. Mar. Sci.}, year = {2015}, volume = {72}, number = {1}, pages = {7--18}, month = jan } @article{Reuter:2003wm, author = {Reuter, N and Hinsen, K and Lacapere, JJ}, title = {{The nature of the low-frequency normal modes of the E1lCa form of the SERCA1 Ca2+-ATPase}}, journal = {Ann Ny Acad Sci}, year = {2003}, volume = {986}, pages = {344--346} } @article{Pogozheva:2014bh, author = {Pogozheva, Irina D and Mosberg, Henry I and Lomize, Andrei L}, title = {{Life at the border: Adaptation of proteins to anisotropic membrane environment}}, journal = {Protein Sci.}, year = {2014}, volume = {23}, number = {9}, pages = {1165--1196}, month = jul } @article{Milne:2013ki, author = {Milne, Jacqueline L S and Borgnia, Mario J and Bartesaghi, Alberto and Tran, Erin E H and Earl, Lesley A and Schauder, David M and Lengyel, Jeffrey and Pierson, Jason and Patwardhan, Ardan and Subramaniam, Sriram}, title = {{Cryo-electron microscopy--a primer for the non-microscopist.}}, journal = {Febs J}, year = {2013}, volume = {280}, number = {1}, pages = {28--45}, month = jan } @article{Rigazio:2000iq, author = {Rigazio, L and Tsakam, B and Junqua, J-C}, title = {{An optimal Bhattacharyya centroid algorithm for Gaussian clustering with applications in automatic speech recognition}}, journal = {Proc IEEE Int Conf Acoust Speech Signal Process}, year = {2000}, volume = {3}, pages = {1599--1593}, month = jun } @article{Skolnick:2009hc, author = {Skolnick, Jeffrey and Arakaki, Adrian K and Lee, Seung Yup and Brylinski, Michal}, title = {{The continuity of protein structure space is an intrinsic property of proteins}}, journal = {Proc. Natl. Acad. Sci. U. S. A.}, year = {2009}, volume = {106}, number = {37}, pages = {15690--15695} } @article{Weikl:2009ki, author = {Weikl, Thomas R. and von Deuster, Carola}, title = {{Selected-fit versus induced-fit protein binding: Kinetic differences and mutational analysis}}, journal = {Proteins: Struct., Funct., Bioinf.}, year = {2009}, volume = {75}, number = {1}, pages = {104--110} } @article{Lyons:2012bp, author = {Lyons, Paul A and Rayner, Tim F and Trivedi, Sapna and Holle, Julia U and Watts, Richard A and Jayne, David R W and Baslund, Bo and Brenchley, Paul and Bruchfeld, Annette and Chaudhry, Afzal N and Cohen Tervaert, Jan Willem and Deloukas, Panos and Feighery, Conleth and Gross, Wolfgang L and Guillevin, Loic and Gunnarsson, Iva and Harper, Lorraine and Hru{\v s}kov{\'a}, Zdenka and Little, Mark A and Martorana, Davide and Neumann, Thomas and Ohlsson, Sophie and Padmanabhan, Sandosh and Pusey, Charles D and Salama, Alan D and Sanders, Jan-Stephan F and Savage, Caroline O and Segelmark, M{\aa}rten and Stegeman, Coen A and Tesa{\v{r}}, Vladimir and Vaglio, Augusto and Wieczorek, Stefan and Wilde, Benjamin and Zwerina, Jochen and Rees, Andrew J and Clayton, David G and Smith, Kenneth G C}, title = {{Genetically Distinct Subsets within ANCA-Associated Vasculitis}}, journal = {N Engl J Med}, year = {2012}, volume = {367}, number = {3}, pages = {214--223}, month = jul } @webpage{Anonymous:JTiPEt5W, title = {{Poisson-Boltzmann}}, url = {http://www.math.fsu.edu/~quine/biotopics07/PB.pdf} } @article{Meier:2007ci, author = {Meier, Sebastian and {\"O}zbek, Suat}, title = {{A biological cosmos of parallel universes: Does protein structural plasticity facilitate evolution?}}, journal = {Bioessays}, year = {2007}, volume = {29}, number = {11}, pages = {1095--1104}, month = nov } @article{McCarty:2009vd, author = {McCarty, Nolan and Meirowitz, Adam}, title = {{Political Game Theory}}, year = {2009}, pages = {1--415}, month = jun } @article{Nguyen:2011fg, author = {Nguyen, M N and Tan, K P and Madhusudhan, M S}, title = {{CLICK--topology-independent comparison of biomolecular 3D structures}}, journal = {Nucleic Acids Res.}, year = {2011}, volume = {39}, number = {Web Server}, pages = {W24--W28}, month = jun } @article{Lumb:2011bw, author = {Lumb, Craig N and He, Ju and Xue, Yi and Stansfeld, Phillip J and Stahelin, Robert V and Kutateladze, Tatiana G and Sansom, Mark S P}, title = {{Biophysical and Computational Studies of Membrane Penetration by the GRP1 Pleckstrin Homology Domain}}, journal = {Structure}, year = {2011}, volume = {19}, number = {9}, pages = {1338--1346}, month = sep } @article{Frazier:2003wf, author = {Frazier, A A and Roller, C R and Havelka, J J and Hinderliter, A}, title = {{Membrane-Bound Orientation and Position of the Synaptotagmin I C2A Domain by Site-Directed Spin Labeling - Biochemistry (ACS Publications)}}, journal = {Biochemistry}, year = {2003} } @article{HOLM:1992uv, author = {HOLM, L and Ouzounis, C and SANDER, C and TUPAREV, G and VRIEND, G}, title = {{A Database of Protein-Structure Families with Common Folding Motifs}}, journal = {Protein Sci.}, year = {1992}, volume = {1}, number = {12}, pages = {1691--1698} } @article{Fox:2014vx, author = {Fox, Naomi K and Brenner, Steven E. and Chandonia, John-Marc}, title = {{SCOPe: Structural Classification of Proteins{\textemdash}extended, integrating SCOP and ASTRAL data and classification of new structures}}, journal = {Nucleic Acids Res.}, year = {2014} } @article{Yang:2005ew, author = {Yang, L and Bahar, I}, title = {{Coupling between Catalytic Site and Collective Dynamics: A Requirement for Mechanochemical Activity of Enzymes}}, journal = {Structure}, year = {2005}, volume = {13}, number = {6}, pages = {893--904}, month = jun } @article{Roy:2011bu, author = {Roy, Christopher J and Oberkampf, William L}, title = {{A comprehensive framework for verification, validation, and uncertainty quantification in scientific computing}}, journal = {Computer Methods in Applied Mechanics and Engineering}, year = {2011}, volume = {200}, number = {25-28}, pages = {2131--2144}, month = jun } @article{Swartz:1995wr, author = {Swartz, K J and MacKinnon, R}, title = {{An inhibitor of the Kv2.1 potassium channel isolated from the venom of a Chilean tarantula.}}, journal = {Neuron}, year = {1995}, volume = {15}, number = {4}, pages = {941--949}, month = oct } @article{JWPonder:2004tn, author = {JWPonder}, title = {{Tinker - manual}}, year = {2004}, pages = {1--213}, month = jul } @article{Avigad:2009ub, author = {Avigad, Jeremy}, title = {{G{\"o}del and the metamathematical tradition}}, year = {2009}, pages = {1--18}, month = jun } @article{Zhang:2003es, author = {Zhang, W and Crocker, E and McLaughlin, S and Smith, S O}, title = {{Binding of Peptides with Basic and Aromatic Residues to Bilayer Membranes: PHENYLALANINE IN THE MYRISTOYLATED ALANINE-RICH C KINASE SUBSTRATE EFFECTOR DOMAIN PENETRATES INTO THE HYDROPHOBIC CORE OF THE BILAYER}}, journal = {J. Biol. Chem.}, year = {2003}, volume = {278}, number = {24}, pages = {21459--21466}, month = jun } @article{Marianayagam:2005vma, author = {Marianayagam, N and Jackson, S}, title = {{Native-state dynamics of the ubiquitin family: implications for function and evolution}}, journal = {Journal of The Royal Society Interface}, year = {2005} } @article{Rokas:2008wt, author = {Rokas, A}, title = {{The origins of multicellularity and the early history of the genetic toolkit for animal development}}, journal = {Annual Review of Genetics}, year = {2008}, volume = {42}, pages = {235--251} } @article{Sutto:2013wh, author = {Sutto, Ludovico and Gervasio, Francesco Luigi}, title = {{Effects of oncogenic mutations on the conformational free-energy landscape of EGFR kinase}}, journal = {{\ldots} of the National Academy of Sciences}, year = {2013} } @article{Wigley:2002ck, author = {Wigley, W Christian and Corboy, Michael J and Cutler, Todd D and Thibodeau, Patrick H and Oldan, Jorge and Lee, Min Goo and Rizo, Josep and Hunt, John F and Thomas, Philip J}, title = {{A protein sequence that can encode native structure by disfavoring alternate conformations}}, journal = {Nat. Struct Biol.}, year = {2002}, pages = {8}, month = apr } @article{Montague:2014ig, author = {Montague, T G and Cruz, J M and Gagnon, J A and Church, G M and Valen, E}, title = {{CHOPCHOP: a CRISPR/Cas9 and TALEN web tool for genome editing}}, journal = {Nucleic Acids Res.}, year = {2014}, volume = {42}, number = {W1}, pages = {W401--W407}, month = jul } @article{Gruschus:2014is, author = {Gruschus, James M and Byrd, R Andrew and Randazzo, Paul A}, title = {{The Importance of Seeing Surface (Effects)}}, journal = {Structure}, year = {2014}, volume = {22}, number = {3}, pages = {363--365}, month = mar } @article{Pirovano:2008kq, author = {Pirovano, Walter and Feenstra, K. Anton and Heringa, Jaap}, title = {{The meaning of alignment: lessons from structural diversity}}, journal = {BMC Bioinformatics}, year = {2008}, volume = {9}, pages = {--} } @article{Treil:2009vz, author = {Treil, Sergei}, title = {{Linear Algebra Done Wrong}}, year = {2009}, pages = {1--264}, month = dec } @article{Janin:2008ha, author = {Janin, Jo{\"e}l and Bahadur, Ranjit P and Chakrabarti, Pinak}, title = {{Protein{\textendash}protein interaction and quaternary structure}}, journal = {Quart. Rev. Biophys.}, year = {2008}, volume = {41}, number = {02}, pages = {133--180}, month = sep } @article{Gjosaeter:1995jp, author = {Gj{\o}s{\ae}ter, Harald}, title = {{Pelagic Fish and the Ecological Impact of the Modern Fishing Industry in the Barents Sea}}, journal = {ARCTIC}, year = {1995}, volume = {48}, number = {3}, pages = {267--278}, month = jan } @techreport{Hwang:2011uo, author = {Hwang, Jenn-Kang}, title = {{Preprint - Derive protein dynamical properties directly from protein structures}}, year = {2011}, month = sep } @article{Moritsugu:2008hc, author = {Moritsugu, Kei and Smith, Jeremy C}, title = {{REACH coarse-grained biomolecular simulation: transferability between different protein structural classes}}, journal = {Biophys. J.}, year = {2008}, volume = {95}, number = {4}, pages = {1639--1648}, month = aug } @article{Milne:2009ts, author = {Milne, JS}, title = {{Group Theory}}, year = {2009}, pages = {1--127}, month = sep } @article{Salzberg:1997te, author = {Salzberg, S}, title = {{On comparing classifiers: Pitfalls to avoid and a recommended approach}}, journal = {Data Mining and Knowledge Discovery}, year = {1997} } @article{Zeldovich:2008wt, author = {Zeldovich, KB and Shakhnovich, EI}, title = {{Understanding protein evolution: from protein physics to Darwinian selection}}, year = {2008} } @article{BaezaDelgado:2012hu, author = {Baeza-Delgado, Carlos and Marti-Renom, Marc A and Mingarro, Ismael}, title = {{Structure-based statistical analysis of transmembrane helices}}, journal = {Eur Biophys J}, year = {2012}, volume = {42}, number = {2-3}, pages = {199--207}, month = may } @article{Rodgers:2013ht, author = {Rodgers, Thomas L and Townsend, Philip D and Burnell, David and Jones, Matthew L and Richards, Shane A and McLeish, Tom C B and Pohl, Ehmke and Wilson, Mark R and Cann, Martin J}, title = {{Modulation of Global Low-Frequency Motions Underlies Allosteric Regulation: Demonstration in CRP/FNR Family Transcription Factors}}, journal = {PLoS Biol}, year = {2013}, volume = {11}, number = {9}, pages = {e1001651}, month = sep } @article{Chrysina:2000jd, author = {Chrysina, E D and Brew, K and Acharya, K R}, title = {{Crystal Structures of Apo- and Holo-bovine ~-Lactalbumin at 2.2-A Resolution Reveal an Effect of Calcium on Inter-lobe Interactions}}, journal = {J. Biol. Chem.}, year = {2000}, volume = {275}, number = {47}, pages = {37021--37029}, month = nov } @article{Fletcher:2002tb, author = {Fletcher, NH}, title = {{Harmonic? Anharmonic? Inharmonic?}}, journal = {American Journal of Physics}, year = {2002}, volume = {70}, pages = {1205} } @article{Skjaerven:2007fi, author = {Skjaerven, Lars and Jonassen, Inge and Reuter, Nathalie}, title = {{TMM@: a web application for the analysis of transmembrane helix mobility}}, journal = {BMC Bioinformatics}, year = {2007}, volume = {8}, pages = {232} } @article{Anonymous:OvLkpYID, title = {{Eigenaanalysis}}, year = {2010}, pages = {1--13}, month = feb } @article{Matheron:1973tn, author = {Matheron, G}, title = {{The Intrinsic Random Functions and Their Applications}}, journal = {Advances in Applied Probability}, year = {1973}, volume = {5}, number = {3}, pages = {439--468} } @article{Martin:1978cz, author = {Martin, J E and Eichinger, B E}, title = {{Distribution functions for Gaussian molecules. I. Stars and random regular nets}}, journal = {J. Chem. Phys.}, year = {1978}, volume = {69}, number = {10}, pages = {4588} } @article{Reuter:2003vr, author = {Reuter, N and Hinsen, K and Lacapere, JJ}, title = {{Normal mode analysis of the Ca2+-ATPase based on a comparison between the E1Ca and E2TG structures}}, journal = {Biophys. J.}, year = {2003}, volume = {84}, number = {2}, pages = {264A--265A} } @article{Taylor:5J0VjX6X, author = {Taylor, WR}, title = {{tayor_2002_supp_info}}, year = {2002}, pages = {6} } @article{Hayek:1974un, author = {Hayek, Friedrich August von}, title = {{The Pretence of Knowledge}}, journal = {Friedrich August von Hayek}, year = {1974}, pages = {1--5} } @article{Cheng:2008wp, author = {Cheng, Eugenia}, title = {{Logic vs illogic: why mathematics is easy and life is hard}}, year = {2008}, pages = {1--26}, month = dec } @article{Mancheno:2003ur, author = {Manche{\~n}o, J M and Martı́n-Benito, J and Martı́nez-Ripoll, M}, title = {{Crystal and Electron Microscopy Structures of Sticholysin II Actinoporin Reveal Insights into the Mechanism of Membrane Pore Formation}}, journal = {Structure}, year = {2003} } @article{Ferrara:2001bj, author = {Ferrara, Philippe and Apostolakis, Joannis and Caflisch, Amedeo}, title = {{Evaluation of a fast implicit solvent model for molecular dynamics simulations}}, journal = {Proteins: Struct., Funct., Bioinf.}, year = {2001}, volume = {46}, number = {1}, pages = {24--33}, month = dec } @article{Stevens:2004jp, author = {Stevens, D L and Olsen, A R}, title = {{Spatially balanced sampling of natural resources}}, journal = {Journal of the American Statistical Association}, year = {2004}, volume = {99}, number = {465}, pages = {262--278}, month = mar } @article{Zen:2008bt, author = {Zen, Andrea and Carnevale, Vincenzo and Lesk, Arthur M. and Micheletti, Christian}, title = {{Correspondences between low-energy modes in enzymes: Dynamics-based alignment of enzymatic functional families}}, journal = {Protein Sci.}, year = {2008}, volume = {17}, number = {5}, pages = {918--929}, month = mar } @article{May:ve, author = {May, Ali and Pool, Ren{\'e} and van Dijk, Erik and Bijlard, Jochem and Abeln, Sanne and Heringa, Jaap and Feenstra, K. Anton}, title = {{Coarse-grained versus atomistic simulations: realistic interaction free energies for real proteins}}, journal = {bioinformatics.oxfordjournals.org} } @article{Feng:2003ik, author = {Feng, J and Bradley, W D and Roberts, M F}, title = {{Optimizing the Interfacial Binding and Activity of a Bacterial Phosphatidylinositol-specific Phospholipase C}}, journal = {J. Biol. Chem.}, year = {2003}, volume = {278}, number = {27}, pages = {24651--24657}, month = jul } @article{Park:2016kw, author = {Park, Mi-Jeong and Sheng, Ren and Silkov, Antonina and Jung, Da-Jung and Wang, Zhi-Gang and Xin, Yao and Kim, Hyunjin and Thiagarajan-Rosenkranz, Pallavi and Song, Seohyeon and Yoon, Youngdae and Nam, Wonhee and Kim, Ilshin and Kim, Eui and Lee, Dong-Gyu and Chen, Yong and Singaram, Indira and Wang, Li and Jang, Myoung Ho and Hwang, Cheol-Sang and Honig, Barry and Ryu, Sungho and Lorieau, Justin and Kim, You-Me and Cho, Wonhwa}, title = {{SH2 Domains Serve as Lipid-Binding Modules for pTyr-Signaling Proteins}}, journal = {Mol. Cell}, year = {2016}, volume = {62}, number = {1}, pages = {7--20}, month = apr } @article{Kailath:1967us, author = {Kailath, T}, title = {{IEEE Xplore Download}}, journal = {Communication Technology}, year = {1967} } @article{Bhattacharyya:1943vk, author = {Bhattacharyya, A}, title = {{On a measure of divergence between two multinomial populations}}, journal = {Sankhy{\=a}: The Indian Journal of Statistics}, year = {1943}, volume = {7}, pages = {401--406}, month = jul } @article{POMORSKI:2001dw, author = {POMORSKI, T and HRAFNSDOTTIR, S and DEVAUX, P and MEER, G}, title = {{Lipid distribution and transport across cellular membranes}}, journal = {Seminars in Cell {\&} Developmental Biology}, year = {2001}, volume = {12}, number = {2}, pages = {139--148}, month = apr } @article{Dai:2011hj, author = {Dai, Liang and Zhou, Yaoqi}, title = {{Characterizing the Existing and Potential Structural Space of Proteins by Large-Scale Multiple Loop Permutations}}, journal = {J. Mol. Biol.}, year = {2011}, volume = {408}, number = {3}, pages = {585--595}, month = may } @article{Eichinger:1980gy, author = {Eichinger, B E}, title = {{Configuration Statistics of Gaussian Molecules}}, journal = {Macromolecules}, year = {1980}, volume = {13}, number = {1}, pages = {1--11}, month = jan } @article{HirstDavid:2012ir, author = {{HirstDavid} and {StorvikGeir} and {RognebakkeHanne} and {AldrinMagne} and {AanesSondre} and Helge, V{\o}lstadJon}, title = {{A Bayesian modelling framework for the estimation of catch-at-age of commercially harvested fish species}}, journal = {Canadian Journal of Fisheries and Aquatic Sciences}, year = {2012}, volume = {69}, number = {12}, pages = {2064--2076}, month = nov } @article{Neale:2011jt, author = {Neale, Chris and Bennett, W F Drew and Tieleman, D Peter and Pom{\`e}s, R{\'e}gis}, title = {{Statistical Convergence of Equilibrium Properties in Simulations of Molecular Solutes Embedded in Lipid Bilayers}}, journal = {J Chem Theory Comput}, year = {2011}, volume = {7}, number = {12}, pages = {4175--4188}, month = dec } @webpage{Anonymous:4R-DFx6d, title = {{PLOS Computational Biology: Structure-Based Statistical Mechanical Model Accounts for the Causality and Energetics of Allosteric Communication}}, url = {http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004678} } @article{Quemeneur:vg, title = {{Shape matters in protein mobility within membranes}}, journal = {pnas.org} } @article{Petrone:2006bn, author = {Petrone, Paula and Pande, Vijay S}, title = {{Can conformational change be described by only a few normal modes?}}, journal = {Biophys. J.}, year = {2006}, volume = {90}, number = {5}, pages = {1583--1593}, month = mar } @article{Fukuchi:2001bv, author = {Fukuchi, S and Nishikawa, K}, title = {{Protein surface amino acid compositions distinctively differ between thermophilic and mesophilic bacteria.}}, journal = {J. Mol. Biol.}, year = {2001}, volume = {309}, number = {4}, pages = {835--843}, month = jun } @article{Wolfenden:D8zp0Wxc, author = {Wolfenden, Richard}, title = {{Experimental Measures of Amino Acid Hydrophobicity and the Topology of Transmembrane and Globular Proteins}}, journal = {jgp.rupress.org} } @article{Kessel:2010wb, author = {Kessel, Amit}, title = {{Introduction to Proteins}}, year = {2010}, pages = {1--621}, month = dec } @webpage{Anonymous:BH05l34D, title = {{Electrostatic Control of the Membrane Targeting of C2 Domains}}, url = {http://www.sciencedirect.com/science/article/pii/S1097276501004269} } @article{Yang:2006ty, author = {Yang, Lee-Wei and Rader, A J and Liu, Xiong and Jursa, Cristopher Jon and Chen, Shann Ching and Karimi, Hassan A and Bahar, Ivet}, title = {{oGNM: online computation of structural dynamics using the Gaussian Network Model}}, journal = {Nucleic Acids Res.}, year = {2006}, volume = {34}, number = {Web Server issue}, pages = {W24--W31} } @article{Toncrova:2010id, author = {Toncrova, Hedvika and McLeish, Tom C B}, title = {{Substrate-Modulated Thermal Fluctuations Affect Long-Range Allosteric Signaling in Protein Homodimers: Exemplified in CAP}}, journal = {Biophys. J.}, year = {2010}, volume = {98}, number = {10}, pages = {2317--2326} } @article{Li:2012ce, author = {Li, Jing and Motlagh, Hesam N and Chakuroff, Carolyn and Thompson, E Brad and Hilser, Vincent J}, title = {{Thermodynamic dissection of the intrinsically disordered N-terminal domain of human glucocorticoid receptor.}}, journal = {J. Biol. Chem.}, year = {2012}, volume = {287}, number = {32}, pages = {26777--26787}, month = aug } @article{Harder:2012fc, author = {Harder, Tim and Borg, Mikael and Bottaro, Sandro and Boomsma, Wouter and Olsson, Simon and Ferkinghoff-Borg, Jesper and Hamelryck, Thomas}, title = {{An Efficient Null Model for Conformational Fluctuations in Proteins}}, journal = {Structure}, year = {2012}, volume = {20}, number = {6}, pages = {1028--1039}, month = jun } @article{Suhre:2004fo, author = {Suhre, Karsten and Sanejouand, Yves-Henri}, title = {{ElNemo: a normal mode web server for protein movement analysis and the generation of templates for molecular replacement}}, journal = {Nucleic Acids Res.}, year = {2004}, volume = {32}, number = {Web Server}, pages = {W610--W614}, month = jul } @article{Itoh:2005cp, author = {Itoh, Toshiki and Erdmann, Kai S and Roux, Aurelien and Habermann, Bianca and Werner, Hauke and De Camilli, Pietro}, title = {{Dynamin and the Actin Cytoskeleton Cooperatively Regulate Plasma Membrane Invagination by BAR and F-BAR Proteins}}, journal = {Developmental Cell}, year = {2005}, volume = {9}, number = {6}, pages = {791--804}, month = dec } @article{Tompa:2012dg, author = {Tompa, Peter}, title = {{Intrinsically disordered proteins: a 10-year recap}}, journal = {Trends in Biochemical Sciences}, year = {2012}, volume = {37}, number = {12}, pages = {509--516}, month = dec } @article{Fangel:2015kc, author = {Fangel, Kirstin and Aas, {\O}ystein and V{\o}lstad, Jon Helge and B{\ae}rum, Kim Magnus and Christensen-Dalsgaard, Signe and Nedreaas, Kjell and Overvik, Modulf and Wold, Line Camilla and Anker-Nilssen, Tycho}, title = {{Assessing incidental bycatch of seabirds in Norwegian coastal commercial fisheries: Empirical and methodological lessons}}, journal = {Global Ecology and Conservation}, year = {2015}, volume = {4}, pages = {127--136}, month = jul } @article{Schuyler:tw, author = {Schuyler, Adam D and Carlson, Heather A and Feldman, Eva L}, title = {{Computational Methods for Predicting Sites of Functionally Important Dynamics}} } @article{Emperador:2008fe, author = {Emperador, Agusti and Meyer, Tim and Orozco, Modesto}, title = {{United-Atom Discrete Molecular Dynamics of Proteins Using Physics-Based Potentials}}, journal = {J Chem Theory Comput}, year = {2008}, volume = {4}, number = {12}, pages = {2001--2010} } @article{CorbalanGarcia:2003ba, author = {Corbal{\'a}n-Garc{\'\i}a, Senena and S{\'a}nchez-Carrillo, Susana and Garc{\'\i}a-Garc{\'\i}a, Josefa and G{\'o}mez-Fern{\'a}ndez, Juan C}, title = {{Characterization of the Membrane Binding Mode of the C2 Domain of PKC$\varepsilon$ {\dag}}}, journal = {Biochemistry}, year = {2003}, volume = {42}, number = {40}, pages = {11661--11668}, month = oct } @article{Williams:2000vn, author = {Williams, R L}, title = {{A note on robust variance estimation for cluster-correlated data}}, journal = {Biometrics}, year = {2000}, volume = {56}, number = {2}, pages = {645--646}, month = jun } @article{Potti:2007ul, author = {Potti, A and Nevins, JR}, title = {{Reply to'Microarrays: retracing steps'}}, journal = {Nature Medicine}, year = {2007}, volume = {13}, number = {11}, pages = {1277--1278} } @article{Riccardi:2010di, author = {Riccardi, Demian and Cui, Qiang and Phillips, Jr, George N}, title = {{Evaluating elastic network models of crystalline biological molecules with temperature factors, correlated motions, and diffuse X-Ray scattering}}, journal = {Biophys. J.}, year = {2010}, volume = {99}, number = {8}, pages = {2616--2625}, month = oct } @article{Granata:2016cu, author = {Granata, Daniele and Carnevale, Vincenzo}, title = {{Accurate Estimation of the Intrinsic Dimension Using Graph Distances: Unraveling the Geometric Complexity of Datasets}}, journal = {Sci. Rep.}, year = {2016}, volume = {6}, pages = {31377}, month = aug } @webpage{Rdogers:QQBLdoH1, author = {Rdogers, Thomas L and Burnell, David and Townsend, Phil D and Pohl, Ehmke and Cann, Martin J and Wilson, Mark R and McLeish, Tom C B}, title = {{$\Delta$$\Delta$PT: a comprehensive toolbox for the analysis of protein motion}}, url = {http://www.biomedcentral.com/1471-2105/14/183/abstract} } @article{Kass:2011it, author = {Kass, Itamar and Reboul, Cyril F and Buckle, Ashley M}, title = {{Computational methods for studying serpin conformational change and structural plasticity.}}, journal = {Meth. Enzymol.}, year = {2011}, volume = {501}, pages = {295--323} } @article{Orlova:2002cw, author = {Orlova, E L and Ushakov, N G and Nesterova, V N and Boitsov, V D}, title = {{ Food supply and feeding of capelin ( Mallotus villosus ) of different size in the central latitudinal zone of the Barents Sea during intermediate and warm years}}, journal = {ICES J. Mar. Sci.}, year = {2002}, volume = {59}, number = {5}, pages = {968--975}, month = jan } @article{Klemm:2012dj, author = {Klemm, Konstantin and Serrano, M {\'A}ngeles and Egu{\'\i}luz, V{\'\i}ctor M and Miguel, Maxi San}, title = {{A measure of individual role in collective dynamics}}, journal = {Sci. Rep.}, year = {2012}, volume = {2}, month = feb } @book{Shannon:1949up, author = {Shannon, C E}, title = {{Bell System Tech. J. 27, 379, 623 (1948)}}, publisher = {A Mathematical Theory of Communication}, year = {1949} } @article{Goh:2016hv, author = {Goh, Boon Chong and Wu, Huixing and Rynkiewicz, Michael J and Schulten, Klaus and Seaton, Barbara A and McCormack, Francis X}, title = {{Elucidation of Lipid Binding Sites on Lung Surfactant Protein A Using X-ray Crystallography, Mutagenesis, and Molecular Dynamics Simulations}}, journal = {Biochemistry}, year = {2016}, pages = {acs.biochem.6b00048}, month = jun } @article{Anonymous:uy3H-Tqw, title = {{Subbey_Main.dvi}}, year = {2017}, pages = {1--11}, month = mar } @article{Noy:2006ws, author = {Noy, A and Meyer, T and Rueda, M and Ferrer, C and Valencia, A and Perez, A and de la Cruz, X and Lopez-Bes, JM and Pouplana, R and Fernandez-Recio, J and Luque, JF and Orozco, M}, title = {{Data mining of molecular dynamics trajectories of nucleic acids}}, journal = {J Biomol Struct Dyn}, year = {2006}, volume = {23}, number = {4}, pages = {447--455} } @article{Vogler:2008ch, author = {V{\"o}gler, Oliver and Barcel{\'o}, Juana M and Ribas, Catalina and Escrib{\'a}, Pablo V}, title = {{Membrane interactions of G proteins and other related proteins}}, journal = {Biochimica et Biophysica Acta (BBA) - Biomembranes}, year = {2008}, volume = {1778}, number = {7-8}, pages = {1640--1652}, month = jul } @article{Schaeffer:2011hl, author = {Schaeffer, R D and Daggett, V}, title = {{Protein folds and protein folding}}, journal = {Protein Eng Des Sel}, year = {2011}, volume = {24}, number = {1-2}, pages = {11--19} } @article{NathJha:2010gj, author = {Nath Jha, Anupam and Vishveshwara, Saraswathi and Banavar, Jayanth R}, title = {{Amino acid interaction preferences in proteins}}, journal = {Protein Sci.}, year = {2010}, volume = {19}, number = {3}, pages = {603--616}, month = feb } @article{Rieping:2005dc, author = {Rieping, W and Habeck, M and Nilges, M}, title = {{Inferential structure determination}}, journal = {Science}, year = {2005}, volume = {309}, number = {5732}, pages = {303--306} } @article{Dashti:vn, author = {Dashti, Ali and Schwander, Peter and Langlois, Robert and Fung, Russell and Li, Wen and Hosseinizadeh, Ahmad and Liao, Hstau Y and Pallesen, Jesper and Sharma, Gyanesh and Stupina, Vera A and Simon, Anne E and Dinman, Jonathan D and Frank, Joachim and Ourmazd, Abbas}, title = {{Trajectories of the ribosome as a Brownian nanomachine}}, journal = {pnas.org} } @article{Maritan:2000vs, author = {Maritan, A and Micheletti, C and Trovato, A and Banavar, JR}, title = {{Optimal shapes of compact strings}}, journal = {Nature}, year = {2000}, volume = {406}, number = {6793}, pages = {287--290} } @webpage{Anonymous:5njB8dtO, title = {{Construction and validation of an atomic model for bacterial TSPO from electron microscopy density, evolutionary constraints, and biochemical and biophysical data}}, url = {http://www.sciencedirect.com/science/article/pii/S0005273614003630} } @article{Feng:2002fc, author = {Feng, J}, title = {{Role of Tryptophan Residues in Interfacial Binding of Phosphatidylinositol-specific Phospholipase C}}, journal = {J. Biol. Chem.}, year = {2002}, volume = {277}, number = {22}, pages = {19867--19875}, month = mar } @article{Kinney:2014ex, author = {Kinney, J B and Atwal, G S}, title = {{Equitability, mutual information, and the maximal information coefficient}}, journal = {Proc. Natl. Acad. Sci. U. S. A.}, year = {2014}, volume = {111}, number = {9}, pages = {3354--3359}, month = mar } @article{Kohout:2003bs, author = {Kohout, Susy C and Corbal{\'a}n-Garc{\'\i}a, Senena and G{\'o}mez-Fern{\'a}ndez, Juan C and Falke, Joseph J}, title = {{C2 Domain of Protein Kinase C$\alpha$:~ Elucidation of the Membrane Docking Surface by Site-Directed Fluorescence and Spin Labeling {\dag}}}, journal = {Biochemistry}, year = {2003}, volume = {42}, number = {5}, pages = {1254--1265}, month = feb } @article{Lavine:2009ub, author = {Lavine, Michael}, title = {{introduction to statistical thought}}, year = {2009}, pages = {1--468}, month = aug } @article{Hajjar:2010br, author = {Hajjar, Eric and Broemstrup, Torben and Kantari, Chahrazade and Witko-Sarsat, Veronique and Reuter, Nathalie}, title = {{Structures of human proteinase 3 and neutrophil elastase - so similar yet so different}}, journal = {Febs J}, year = {2010}, volume = {277}, number = {10}, pages = {2238--2254} } @article{Anderluh:2008bi, author = {Anderluh, Gregor and Lakey, Jeremy H}, title = {{Disparate proteins use similar architectures to damage membranes}}, journal = {Trends in Biochemical Sciences}, year = {2008}, volume = {33}, number = {10}, pages = {482--490}, month = oct } @article{Cutsforth:1989wg, author = {Cutsforth, G A and Whitaker, R N and Hermans, J and Lentz, B R}, title = {{A new model to describe extrinsic protein binding to phospholipid membranes of varying composition: application to human coagulation proteins - Biochemistry (ACS Publications)}}, journal = {Biochemistry}, year = {1989} } @article{Afgan:2016il, author = {Afgan, Enis and Baker, Dannon and van den Beek, Marius and Blankenberg, Daniel and Bouvier, Dave and {\v C}ech, Martin and Chilton, John and Clements, Dave and Coraor, Nate and Eberhard, Carl and Gr{\"u}ning, Bj{\"o}rn and Guerler, Aysam and Hillman-Jackson, Jennifer and Von Kuster, Greg and Rasche, Eric and Soranzo, Nicola and Turaga, Nitesh and Taylor, James and Nekrutenko, Anton and Goecks, Jeremy}, title = {{The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update.}}, journal = {Nucleic Acids Res.}, year = {2016}, volume = {44}, number = {W1}, pages = {W3--W10}, month = jul } @article{Tungtur:2011ts, author = {Tungtur, S and Parente, D J}, title = {{Functionally important positions can comprise the majority of a protein's architecture - Tungtur - 2011 - Proteins: Structure, Function, and Bioinformatics - Wiley Online Library}}, journal = {Structure}, year = {2011} } @article{STEVENS:1990vb, author = {Stevens, Raymond C and Gouaux, J Eric and Lipscomb, William N}, title = {{Structural consequences of effector binding to the T-state of aspartate carbamoyltransferase: crystal-structures of the unligated and ATP- and CTP-complexed enzymes at 2.6-{\AA} resolution}}, journal = {Biochemistry}, year = {1990}, volume = {29}, number = {33}, pages = {7691--7701} } @article{Bahar:2009wk, author = {Bahar, I and Lezon, TR and Bakan, A and Shrivastava, IH}, title = {{Normal Mode Analysis of Biomolecular Structures: Functional Mechanisms of Membrane Proteins}}, journal = {Chem. Rev}, year = {2009}, pages = {1--432} } @article{Tresaugues:2014ba, author = {Tr{\'e}saugues, Lionel and Silvander, Camilla and Flodin, Susanne and Welin, Martin and Nyman, Tomas and Gr{\"a}slund, Susanne and Hammarstr{\"o}m, Martin and Berglund, Helena and Nordlund, P{\"a}r}, title = {{Structural Basis for Phosphoinositide Substrate Recognition, Catalysis, and Membrane Interactions in Human Inositol Polyphosphate 5-Phosphatases}}, journal = {Structure}, year = {2014}, volume = {22}, number = {5}, pages = {744--755}, month = may } @article{Choe:2005ic, author = {Choe, Seungho and Sun, Sean X}, title = {{The elasticity of $\alpha$-helices}}, journal = {J. Chem. Phys.}, year = {2005}, volume = {122}, number = {24}, pages = {244912} } @article{Daggett:2003ux, author = {Daggett, V}, title = {{Is there a unifying mechanism for protein folding?}}, journal = {Trends in Biochemical Sciences}, year = {2003} } @article{Ortiz:2000vl, author = {Ortiz, AR and Skolnick, J}, title = {{Sequence evolution and the mechanism of protein folding}}, journal = {Biophys. J.}, year = {2000}, volume = {79}, number = {4}, pages = {1787--1799} } @article{Cossio:2010vs, author = {Cossio, P and Trovato, A and Pietrucci, F and Seno, F}, title = {{Exploring the Universe of Protein Structures beyond the Protein Data Bank}}, journal = {PLoS Comput. Biol.}, year = {2010} } @article{Maguid:2005ec, author = {Maguid, Sandra and Fern{\'a}ndez-Alberti, Sebasti{\'a}n and Echave, Juli{\'a}n}, title = {{Exploring the common dynamics of homologous proteins. Application to the globin family}}, journal = {Biophys. J.}, year = {2005}, volume = {89}, number = {1}, pages = {3--13}, month = jul } @article{Micheletti:2001jz, author = {Micheletti, C and Banavar, JR and Maritan, A}, title = {{Conformations of proteins in equilibrium}}, journal = {Phys. Rev. Lett.}, year = {2001}, volume = {87}, number = {8}, pages = {--} } @article{Chng:2008tz, author = {Chng, C and Yang, L}, title = {{Coarse-Grained Models Reveal Functional Dynamics--II. Molecular Dynamics Simulation at \ldots}}, journal = {Bioinformatics and Biology Insights}, year = {2008} } @article{Ma:2000dw, author = {Ma, Jianpeng and Sigler, Paul B and Xu, Zhaohui and Karplus, Martin}, title = {{A dynamic model for the allosteric mechanism of GroEL}}, journal = {J. Mol. Biol.}, year = {2000}, volume = {302}, number = {2}, pages = {303--313}, month = sep } @article{Atilgan:2009jq, author = {Atilgan, Canan and Atilgan, Ali Rana}, title = {{Perturbation-response scanning reveals ligand entry-exit mechanisms of ferric binding protein.}}, journal = {PLoS Comput. Biol.}, year = {2009}, volume = {5}, number = {10}, pages = {e1000544}, month = oct } @article{Pan:tt, author = {Pan, K M and Baldwin, M and Nguyen, J and Gasset, M and Serban, A and Groth, D and Mehlhorn, I and Huang, Z and Fletterick, R J and Cohen, F E}, title = {{Conversion of alpha-helices into beta-sheets features in the formation of the scrapie prion proteins}}, journal = {sciencedirect.com} } @article{Yang:2015fd, author = {Yang, Boqian and Pu, Mingming and Khan, Hanif M and Friedman, Larry and Reuter, Nathalie and Roberts, Mary F and Gershenson, Anne}, title = {{Quantifying Transient Interactions between BacillusPhosphatidylinositol-Specific Phospholipase-C and Phosphatidylcholine-Rich Vesicles}}, journal = {JACS}, year = {2015}, volume = {137}, number = {1}, pages = {14--17}, month = jan } @article{SekinoSuzuki:1996uy, author = {Sekino-Suzuki, N and Nakamura, M and Mitsui, K I and Ohno-Iwashita, Y}, title = {{Contribution of individual tryptophan residues to the structure and activity of theta-toxin (perfringolysin O), a cholesterol-binding cytolysin.}}, journal = {Eur. J. Biochem.}, year = {1996}, volume = {241}, number = {3}, pages = {941--947}, month = nov } @article{Yu:2016bw, author = {Yu, Yi and Xiao, Gaoxi and Zhou, Jie and Wang, Yubo and Wang, Zhen and Kurths, J{\"u}rgen and Schellnhuber, Hans Joachim}, title = {{System crash as dynamics of complex networks}}, journal = {Proc. Natl. Acad. Sci. U. S. A.}, year = {2016}, volume = {113}, number = {42}, pages = {11726--11731}, month = oct } @article{Melnychuk:2017gh, author = {Melnychuk, Michael C and Peterson, Emily and Elliott, Matthew and Hilborn, Ray}, title = {{Fisheries management impacts on target species status}}, journal = {Proc Natl Acad Sci U S A}, year = {2017}, volume = {114}, number = {1}, pages = {178--183}, month = jan } @article{Sagui:1999wa, author = {Sagui, C and Darden, TA}, title = {{Molecular dynamics simulations of biomolecules: long-range electrostatic effects}}, journal = {Annu Rev Bioph Biom}, year = {1999}, volume = {28}, number = {1}, pages = {155--179} } @article{Micheletti:2002iw, author = {Micheletti, C}, title = {{Elastic Properties of Proteins: Insight on the Folding Process and Evolutionary Selection of Native Structures}}, journal = {J. Mol. Biol.}, year = {2002}, volume = {321}, number = {5}, pages = {909--921}, month = aug } @article{Wong:2010vh, author = {Wong, WC and Maurer-Stroh, S and Eisenhaber, F}, title = {{More Than 1,001 Problems with Protein Domain Databases: Transmembrane Regions, Signal Peptides and the Issue of Sequence Homology}}, journal = {PLoS Comput. Biol.}, year = {2010}, volume = {6}, number = {7}, pages = {e1000867} } @article{Berger:2003th, author = {Berger, J O}, title = {{Could Fisher, Jeffreys and Neyman have agreed on testing?}}, journal = {Statistical Science}, year = {2003}, volume = {18}, number = {1}, pages = {1--32} } @article{Eisenhaber:1995bd, author = {Eisenhaber, Frank and Lijnzaad, Philip and Argos, Patrick and Sander, Chris and Scharf, Michael}, title = {{The double cubic lattice method: Efficient approaches to numerical integration of surface area and volume and to dot surface contouring of molecular assemblies}}, journal = {J. Comput. Chem.}, year = {1995}, volume = {16}, number = {3}, pages = {273--284} } @article{Juraszek:2013ir, author = {Juraszek, J and Saladino, G and van Erp, T and Gervasio, F}, title = {{Efficient Numerical Reconstruction of Protein Folding Kinetics with Partial Path Sampling and Pathlike Variables}}, journal = {Phys. Rev. Lett.}, year = {2013}, volume = {110}, number = {10}, pages = {108106}, month = mar } @article{Sutto:2010df, author = {Sutto, Ludovico and D{\textquoteright}Abramo, Marco and Gervasio, Francesco Luigi}, title = {{Comparing the Efficiency of Biased and Unbiased Molecular Dynamics in Reconstructing the Free Energy Landscape of Met-Enkephalin}}, journal = {J Chem Theory Comput}, year = {2010}, volume = {6}, number = {12}, pages = {3640--3646}, month = dec } @article{Sabass:2016hv, author = {Sabass, Benedikt and Stone, Howard A}, title = {{Role of the Membrane for Mechanosensing by Tethered Channels}}, journal = {Phys. Rev. Lett.}, year = {2016}, volume = {116}, number = {25}, pages = {258101}, month = jun } @book{Anonymous:2002wi, title = {{Current topics in membranes}}, publisher = {Elsevier}, year = {2002} } @article{Stigler:2011ct, author = {Stigler, J and Ziegler, F and Gieseke, A and Gebhardt, J C M and Rief, M}, title = {{The Complex Folding Network of Single Calmodulin Molecules}}, journal = {Science}, year = {2011}, volume = {334}, number = {6055}, pages = {512--516}, month = oct } @article{Nagano:2005wj, author = {Nagano, Nozomi}, title = {{EzCatDB: the Enzyme Catalytic-mechanism Database}}, journal = {Nucleic Acids Res.}, year = {2005} } @article{Amber94, author = {Cornell, W D and Cieplak, P and Bayly, C I and I.R. Gould, I R and Merz Jr, K M and Ferguson, D M and Spellmeyer, D C and Fox, T and Caldwell, J W and Kollman, P A}, title = {{A second generation force field for the simulation of proteins and nucleic acids}}, journal = {J. Am. Chem. Soc.}, year = {1995}, volume = {117}, pages = {5179} } @article{Mallamace:2016jc, author = {Mallamace, Francesco and Corsaro, Carmelo and Mallamace, Domenico and Vasi, Sebastiano and Vasi, Cirino and Baglioni, Piero and Buldyrev, Sergey V and Chen, Sow-Hsin and Stanley, H Eugene}, title = {{Energy landscape in protein folding and unfolding}}, journal = {Proc. Natl. Acad. Sci. U. S. A.}, year = {2016}, volume = {113}, number = {12}, pages = {3159--3163}, month = mar } @unpublished{Fuglebakk:BHKn2tsT, author = {Fuglebakk, Edvin and Reuter, Nathalie and Hinsen, Konrad}, title = {{Inter-residue covariance predictions from protein elastic network models}} } @article{Hinsen:2000vg, author = {Hinsen, K}, title = {{Domain motions in proteins}}, journal = {Journal of Molecular Liquids}, year = {2000}, volume = {84}, number = {1}, pages = {53--63} } @article{Skinner:ts, author = {Skinner, John J and Yu, Wookyung and Gichana, Elizabeth K and Baxa, Michael C and Hinshaw, James R and Freed, Karl F and Sosnick, Tobin R}, title = {{Benchmarking all-atom simulations using hydrogen exchange}}, journal = {pnas.org} } @article{Keskin:2004ft, author = {Keskin, Ozlem and Tsai, Chung-Jung and Wolfson, Haim and Nussinov, Ruth}, title = {{A new, structurally nonredundant, diverse data set of protein-protein interfaces and its implications}}, journal = {Protein Sci.}, year = {2004}, volume = {13}, number = {4}, pages = {1043--1055}, month = apr } @webpage{Anonymous:nrojxBc6, title = {{Commentary: Scientific communication in the digital age}}, url = {http://scitation.aip.org/content/aip/magazine/physicstoday/article/69/6/10.1063/PT.3.3181} } @article{Schervish:1996wo, author = {Schervish, MJ}, title = {{P values: What they are and what they are not}}, journal = {Am Stat}, year = {1996}, volume = {50}, number = {3}, pages = {203--206} } @article{Bahar:2010gf, author = {Bahar, Ivet and Lezon, Timothy R and Yang, Lee-Wei and Eyal, Eran}, title = {{Global dynamics of proteins: bridging between structure and function.}}, journal = {Annu. Rev. Biophys.}, year = {2010}, volume = {39}, pages = {23--42}, month = jun } @article{Nguyen:2011er, author = {Nguyen, M N and Madhusudhan, M S}, title = {{Biological insights from topology independent comparison of protein 3D structures}}, journal = {Nucleic Acids Res.}, year = {2011}, volume = {39}, number = {14}, pages = {e94--e94}, month = aug } @article{Chevrot:2011ba, author = {Chevrot, Guillaume and Calligari, Paolo and Hinsen, Konrad and Kneller, Gerald R}, title = {{Least constraint approach to the extraction of internal motions from molecular dynamics trajectories of flexible macromolecules}}, journal = {J. Chem. Phys.}, year = {2011}, volume = {135}, number = {8}, pages = {084110} } @article{Kessenbrock:2009fh, author = {Kessenbrock, Kai and Krumbholz, Markus and Sch{\"o}nermarck, Ulf and Back, Walter and Gross, Wolfgang L and Werb, Zena and Gr{\"o}ne, Hermann-Josef and Brinkmann, Volker and Jenne, Dieter E}, title = {{Netting neutrophils in autoimmune small-vessel vasculitis}}, journal = {Nature Medicine}, year = {2009}, volume = {15}, number = {6}, pages = {623--625}, month = may } @article{Corkeron:2009im, author = {Corkeron, Peter J}, title = {{Marine mammals' influence on ecosystem processes affecting fisheries in the Barents Sea is trivial}}, journal = {Biology Letters}, year = {2009}, volume = {5}, number = {2}, pages = {204--206}, month = apr } @article{Banavar:2002kk, author = {Banavar, JR and Maritan, A and Micheletti, C and Trovato, A}, title = {{Geometry and physics of proteins}}, journal = {Proteins: Struct., Funct., Bioinf.}, year = {2002}, volume = {47}, number = {3}, pages = {315--322} } @article{BENJAMINI:1988wv, author = {BENJAMINI, Y}, title = {{Opening the Box of a Boxplot}}, journal = {Am Stat}, year = {1988}, volume = {42}, number = {4}, pages = {257--262} } @article{Hajjar:2007fv, author = {Hajjar, Eric and Korkmaz, Brice and Reuter, Nathalie}, title = {{Differences in the substrate binding sites of murine and human proteinase 3 and neutrophil elastase}}, journal = {Febs Lett}, year = {2007}, volume = {581}, number = {29}, pages = {5685--5690} } @article{Zhao:2013ca, author = {Zhao, Gongpu and Perilla, Juan R and Yufenyuy, Ernest L and Meng, Xin and Chen, Bo and Ning, Jiying and Ahn, Jinwoo and Gronenborn, Angela M and Schulten, Klaus and Aiken, Christopher and Zhang, Peijun}, title = {{Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics}}, journal = {Nature}, year = {2013}, volume = {497}, number = {7451}, pages = {643--646}, month = may } @article{Anonymous:xynuDwyO, title = {{Matching}}, year = {2003}, pages = {6} } @article{BenTal:1997gi, author = {Ben-Tal, N and Honig, B and Miller, C and McLaughlin, S}, title = {{Electrostatic binding of proteins to membranes. Theoretical predictions and experimental results with charybdotoxin and phospholipid vesicles}}, journal = {Biophys. J.}, year = {1997}, volume = {73}, number = {4}, pages = {1717--1727}, month = oct } @article{Diethelm:2012tx, author = {Diethelm, Kai}, title = {{The Limits of Reproducibility in Numerical Simulation}}, journal = {Parallel algorithms}, year = {2012}, pages = {1--10} } @article{Anonymous:fU7U8WSb, title = {{Finite differences}}, year = {2004}, pages = {8}, month = nov } @article{Kundu:2002wx, author = {Kundu, Sibsankar and Melton, Julia S and Sorensen, Dan C and Phillips, George N. Jr}, title = {{Dynamics of proteins in crystals: Comparison of experiment with simple models}}, journal = {Biophys. J.}, year = {2002}, volume = {83}, number = {2}, pages = {723--732}, month = aug } @article{Min:2005gj, author = {Min, W and English, BP and Luo, GB and Cherayil, BJ and Kou, SC and Xie, XS}, title = {{Fluctuating enzymes: Lessons from single-molecule studies}}, journal = {Accounts Chem Res}, year = {2005}, volume = {38}, number = {12}, pages = {923--931} } @article{Quillin:2000fo, author = {Quillin, Michael L and Matthews, Brian W}, title = {{Accurate calculation of the density of proteins}}, journal = {Acta Crystallogr D}, year = {2000}, volume = {56}, number = {7}, pages = {791--794}, month = jul } @article{TorresSanchez:2015ws, author = {Torres-S{\'a}nchez, A and Vanegas, J M and Arroyo, M}, title = {{Examining the Mechanical Equilibrium of Microscopic Stresses in Molecular Simulations}}, journal = {Phys. Rev. Lett.}, year = {2015} } @article{Merlino:2003ha, author = {Merlino, A and Vitagliano, L and Ceruso, MA and Mazzarella, L}, title = {{Subtle functional collective motions in pancreatic-like ribonucleases: From ribonuclease A to angiogenin}}, journal = {Proteins: Struct., Funct., Bioinf.}, year = {2003}, volume = {53}, number = {1}, pages = {101--110} } @article{McMahon:2005km, author = {McMahon, Harvey T and Gallop, Jennifer L}, title = {{Membrane curvature and mechanisms of dynamic cell membrane remodelling}}, journal = {Nature}, year = {2005}, volume = {438}, number = {7068}, pages = {590--596}, month = dec } @article{Zeldovich:2006bn, author = {Zeldovich, K and Berezovsky, I and Shakhnovich, E}, title = {{Physical Origins of Protein Superfamilies}}, journal = {J. Mol. Biol.}, year = {2006}, volume = {357}, number = {4}, pages = {1335--1343}, month = apr } @article{Yeh:2014ea, author = {Yeh, So-Wei and Huang, Tsun-Tsao and Liu, Jen-Wei and Yu, Sung-Huan and Shih, Chien-Hua and Hwang, Jenn-Kang and Echave, Juli{\'a}n}, title = {{Local Packing Density Is the Main Structural Determinant of the Rate of Protein Sequence Evolution at Site Level}}, journal = {BioMed Research International}, year = {2014}, volume = {2014}, number = {11}, pages = {1--10} } @article{Kutateladze:2010jz, author = {Kutateladze, Tatiana G}, title = {{Translation of the phosphoinositide code by PI effectors}}, journal = {Nat Chem Biol}, year = {2010}, volume = {6}, number = {7}, pages = {507--513}, month = jul } @article{Heimburg:1995jd, author = {Heimburg, T and Marsh, D}, title = {{Protein surface-distribution and protein-protein interactions in the binding of peripheral proteins to charged lipid membranes}}, journal = {Biophys. J.}, year = {1995}, volume = {68}, number = {2}, pages = {536--546}, month = feb } @article{Lu:2005kq, author = {Lu, Mingyang and Ma, Jianpeng}, title = {{The Role of Shape in Determining Molecular Motions}}, journal = {Biophys. J.}, year = {2005}, volume = {89}, number = {4}, pages = {2395--2401}, month = oct } @article{Thompson:2011it, author = {Thompson, Aaron A and Jiao, Guan-Sheng and Kim, Seongjin and Thai, April and Cregar-Hernandez, Lynne and Margosiak, Stephen A and Johnson, Alan T and Han, Gye Won and O'Malley, Sean S and Stevens, Raymond C RC}, title = {{Structural characterization of three novel hydroxamate-based zinc chelating inhibitors of the Clostridium botulinum serotype A neurotoxin light chain metalloprotease reveals a compact binding site resulting from 60/70 loop flexibility.}}, journal = {Biochemistry}, year = {2011}, volume = {50}, number = {19}, pages = {4019--4028}, month = may } @webpage{Anonymous:EvPMc1vY, title = {{BMC Bioinformatics | Full text | Reviewer acknowledgement 2013}}, url = {http://www.biomedcentral.com/1471-2105/15/67} } @article{Yang:2007en, author = {Yang, Lee-Wei and Eyal, Eran and Chennubhotla, Chakra and Jee, JunGoo and Gronenborn, Angela M and Bahar, Ivet}, title = {{Insights into equilibrium dynamics of proteins from comparison of NMR and X-ray data with computational predictions}}, journal = {Structure}, year = {2007}, volume = {15}, number = {6}, pages = {741--749} } @article{Bahar:1997hf, author = {Bahar, Ivet and Atilgan, Ali Rana and Erman, Burak}, title = {{Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential}}, journal = {Folding Des.}, year = {1997}, volume = {2}, number = {3}, pages = {173--181}, month = jun } @article{CHOTHIA:1986tma, author = {Chothia, Cyrus and LESK, AM}, title = {{The Relation Between the Divergence of Sequence and Structure in Proteins}}, journal = {Embo J}, year = {1986}, volume = {5}, number = {4}, pages = {823--826} } @article{Samson:2011ek, author = {Samson, Abraham O and Levitt, Michael}, title = {{Normal Modes of Prion Proteins: From Native to Infectious Particle}}, journal = {Biochemistry}, year = {2011}, volume = {50}, number = {12}, pages = {2243--2248}, month = mar } @article{Teilum:2009bf, author = {Teilum, Kaare and Olsen, Johan G and Kragelund, Birthe B}, title = {{Functional aspects of protein flexibility}}, journal = {Cell Mol Life Sci}, year = {2009}, volume = {66}, number = {14}, pages = {2231--2247} } @article{Tama:2000tu, author = {Tama, Florence and Gadea, Florent Xavier and Marques, Osni and Sanejouand, Yves-Henri}, title = {{Building-block approach for determining low-frequency normal modes of macromolecules}}, journal = {Proteins: Struct., Funct., Bioinf.}, year = {2000}, volume = {41}, number = {1}, pages = {1--7} } @article{Deleu:2014cq, author = {Deleu, Magali and Crowet, Jean-Marc and Nasir, Mehmet N and Lins, Laurence}, title = {{Complementary biophysical tools to investigate lipid specificity in the interaction between bioactive molecules and the plasma membrane: A review}}, journal = {Biochimica et Biophysica Acta (BBA) - Biomembranes}, year = {2014}, volume = {1838}, number = {12}, pages = {3171--3190}, month = dec } @article{Labarga:2007gw, author = {Labarga, Alberto and Valentin, Franck and Anderson, Mikael and Lopez, Rodrigo}, title = {{Web Services at the European Bioinformatics Institute}}, journal = {Nucleic Acids Res.}, year = {2007}, pages = {gkm291v1}, month = jun } @article{Gerek:2011bi, author = {{Gerek} and {Bolia} and {Ozkan}}, title = {{Perturbation Response Scanning Method for Identifying Allosteric Transitions and Utilizing in Flexible Docking}}, journal = {Biophysj}, year = {2011}, volume = {100}, number = {3}, pages = {0--0}, month = feb } @article{Nivaskumar:2014cl, author = {Nivaskumar, Mangayarkarasi and Bouvier, Guillaume and Campos, Manuel and Nadeau, Nathalie and Yu, Xiong and Egelman, Edward H and Nilges, Michael and Francetic, Olivera}, title = {{Distinct Docking and Stabilization Steps of the Pseudopilus Conformational Transition Path Suggest Rotational Assembly of Type IV Pilus-like Fibers}}, journal = {Structure}, year = {2014}, month = mar } @article{Khataee:2014dy, author = {Khataee, H and Wee-Chung Liew, A}, title = {{A mathematical model describing the mechanical kinetics of kinesin stepping}}, journal = {Bioinformatics}, year = {2014}, volume = {30}, number = {3}, pages = {353--359}, month = jan } @article{Yuan:wk, author = {Yuan, Yue and Tam, Ming F and Simplaceanu, Virgil and Ho, Chien}, title = {{New Look at Hemoglobin Allostery}}, journal = {pubs.acs.org} } @article{Calandrini:2008cq, author = {Calandrini, Vania and Kneller, Gerald R}, title = {{Influence of pressure on the slow and fast fractional relaxation dynamics in lysozyme: A simulation study}}, journal = {J. Chem. Phys.}, year = {2008}, volume = {128}, number = {6}, pages = {065102--065102--8} } @article{Anonymous:uA6kjyuD, title = {{Muskie Lunacy: Does the Lunar Cycle Influence Angler Catch of Muskellunge (Esox masquinongy)?}} } @article{Anderson:1972wi, author = {Anderson, PW}, title = {{More is different}}, journal = {Science}, year = {1972}, volume = {177}, number = {4047}, pages = {393--396} } @article{Hilser:2015dy, author = {Hilser, Vincent J and Anderson, Jeremy A and Motlagh, Hesam N}, title = {{Allostery vs. {\textquotedblleft}allokairy{\textquotedblright}: Fig. 1.}}, journal = {Proc. Natl. Acad. Sci. U. S. A.}, year = {2015}, volume = {112}, number = {37}, pages = {11430--11431}, month = sep } @article{Andreeva:2006ig, author = {Andreeva, Antonina and Murzin, Alexey G}, title = {{Evolution of protein fold in the presence of functional constraints}}, journal = {Current Opinion in Structural Biology}, year = {2006}, volume = {16}, number = {3}, pages = {399--408} } @article{Guth:2005wo, author = {G{\"u}th, Werner and Ivanova-Stenzel, Radosveta and Wolfstetter, Elmar}, title = {{Bidding Behaviour in Asymmetric Auctions: An experimental study}}, year = {2005}, pages = {1--35}, month = nov } @article{Roy:2016ij, author = {Roy, Amitava and Hua, Duy P and Post, Carol Beth}, title = {{Analysis of Multidomain Protein Dynamics}}, journal = {J Chem Theory Comput}, year = {2016}, volume = {12}, number = {1}, pages = {274--280}, month = jan } @article{VelazquezMuriel:2009ik, author = {Velazquez-Muriel, Javier A and Rueda, Manuel and Cuesta, Isabel and Pascual-Montano, Alberto and Orozco, Modesto}, title = {{Comparison of molecular dynamics and superfamily spaces of protein domain deformation}}, journal = {BMC Structural Biology}, year = {2009}, volume = {9}, number = {1}, pages = {6} } @webpage{Anonymous:6OINPeeW, title = {{Interactions of Phospholipid Bilayers with Several Classes of Amphiphilic $\alpha$-Helical Peptides: Insights from Coarse-Grained Molecular Dynamics Simulations - The Journal of Physical Chemistry B (ACS Publications)}}, url = {http://pubs.acs.org/doi/abs/10.1021/jp908320b} } @article{Ma:2004uk, author = {Ma, J}, title = {{New advances in normal mode analysis of supermolecular complexes and applications to structural refinement}}, journal = {Current protein {\&} peptide science}, year = {2004}, volume = {5}, number = {2}, pages = {119} } @article{Pauli:2014ev, author = {Pauli, A and Norris, M L and Valen, E and Chew, G L and Gagnon, J A and Zimmerman, S and Mitchell, A and Ma, J and Dubrulle, J and Reyon, D and Tsai, S Q and Joung, J K and Saghatelian, A and Schier, A F}, title = {{Toddler: An Embryonic Signal That Promotes Cell Movement via Apelin Receptors}}, journal = {Science}, year = {2014}, volume = {343}, number = {6172}, pages = {1248636--1248636}, month = feb } @article{Gross:tz, author = {Gross, Michael}, title = {{Just 15 years ago, the idea that proteins might be functional without a well-ordered 3D structure was heretical. But as Michael Gross discovers, a little flexibility can go a long way}}, journal = {Chemistry World}, pages = {1--4} } @article{VanAalten:1997uwa, author = {VanAalten, DMF and DeGroot, BL and Findlay, JBC and Berendsen, HJC and Amadei, A}, title = {{A comparison of techniques for calculating protein essential dynamics}}, journal = {J. Comput. Chem.}, year = {1997}, volume = {18}, number = {2}, pages = {169--181} } @article{Chen:2000vf, author = {Chen, X and Wolfgang, D E and Sampson, N S}, title = {{Use of the parallax-quench method to determine the position of the active-site loop of cholesterol oxidase in lipid bilayers.}}, journal = {Biochemistry}, year = {2000}, volume = {39}, number = {44}, pages = {13383--13389}, month = nov } @article{Levitt:1998uy, author = {Levitt, M and GERSTEIN, M}, title = {{A unified statistical framework for sequence comparison and structure comparison}}, journal = {Proc. Natl. Acad. Sci. U. S. A.}, year = {1998}, volume = {95}, number = {11}, pages = {5913--5920} } @incollection{Shehu:2013tb, author = {Shehu, Amarda}, title = {{book}}, year = {2013}, pages = {1--60}, month = mar } @article{Hajjar:2006ew, author = {Hajjar, E and Korkmaz, B and Gauthier, F and Brandsdal, BO and Witko-Sarsat, V and Reuter, N}, title = {{Inspection of the binding sites of proteinase3 for the design of a highly specific substrate}}, journal = {J Med Chem}, year = {2006}, volume = {49}, number = {4}, pages = {1248--1260} } @article{Micheletti:2001vk, author = {Micheletti, C and Seno, F and Maritan, A and Banavar, JR}, title = {{An optimal procedure to extract interaction potentials for protein folding}}, journal = {Comp Mater Sci}, year = {2001}, volume = {20}, pages = {305--310} } @article{Li:2005em, author = {Li, Xingong}, title = {{Deriving Directional Variance from Covariance Matrix}}, journal = {Transactions in GIS}, year = {2005}, volume = {9}, number = {3}, pages = {443--445}, month = jun } @article{Perisic:1998tv, author = {Perisic, O and Fong, S and Lynch, D E and Bycroft, M and Williams, R L}, title = {{Crystal structure of a calcium-phospholipid binding domain from cytosolic phospholipase A2.}}, journal = {J. Biol. Chem.}, year = {1998}, volume = {273}, number = {3}, pages = {1596--1604}, month = jan } @article{Mourao:2014ds, author = {Mour{\~a}o, M{\'a}rcio A and Hakim, Joe B and J, Schneider}, title = {{Connecting the Dots: The Effects of Macromolecular Crowding on Cell Physiology}}, journal = {Biophys. J.}, year = {2014}, volume = {107}, number = {12}, pages = {2761--2766}, month = dec } @article{Yomo:1999cq, author = {Yomo, Tetsuya and Saito, Seiji and Sasai, Masaki}, title = {{Gradual development of protein-like global structures through functional selection}}, journal = {Nature Structural {\&} Molecular Biology}, year = {1999}, volume = {6}, number = {8}, pages = {743}, month = aug } @article{Kleinman:2010gw, author = {Kleinman, C L and Rodrigue, N and Lartillot, N and Philippe, H}, title = {{Statistical Potentials for Improved Structurally Constrained Evolutionary Models}}, journal = {Molecular Biology and Evolution}, year = {2010}, volume = {27}, number = {7}, pages = {1546--1560}, month = jul } @article{Lomize:2006gs, author = {Lomize, Mikhail A and Lomize, Andrei L and Pogozheva, Irina D and Mosberg, Henry I}, title = {{OPM: orientations of proteins in membranes database.}}, journal = {Bioinformatics}, year = {2006}, volume = {22}, number = {5}, pages = {623--625}, month = mar } @article{Rohs:2010ej, author = {Rohs, Remo and Jin, Xiangshu and West, Sean M and Joshi, Rohit and Honig, Barry and Mann, Richard S}, title = {{Origins of Specificity in Protein-DNA Recognition}}, journal = {Annu Rev Biochem}, year = {2010}, volume = {79}, number = {1}, pages = {233--269}, month = jun } @article{Illergard:2009cr, author = {Illergard, Kristoffer and Ardell, David H. and Elofison, Arne}, title = {{Structure is three to ten times more conserved than sequence-A study of structural response in protein cores}}, journal = {Proteins: Struct., Funct., Bioinf.}, year = {2009}, volume = {77}, number = {3}, pages = {499--508} } @article{Anonymous:vS6QApXi, title = {{matching}}, year = {2007}, pages = {10} } @article{MacCallum:2011kx, author = {MacCallum, Justin L and Bennett, W F Drew and Tieleman, D Peter}, title = {{Transfer of Arginine into Lipid Bilayers Is Nonadditive}}, journal = {Biophysj}, year = {2011}, volume = {101}, number = {1}, pages = {110--117}, month = jul } @article{Szekely:2007id, author = {Sz{\'e}kely, G{\'a}bor J and Rizzo, Maria L and Bakirov, Nail K}, title = {{Measuring and testing dependence by correlation of distances}}, journal = {The Annals of Statistics}, year = {2007}, volume = {35}, number = {6}, pages = {2769--2794}, month = dec } @article{Zhang:2005doa, author = {Zhang, Y and Skolnick, J}, title = {{TM-align: a protein structure alignment algorithm based on the TM-score}}, journal = {Nucleic Acids Res.}, year = {2005}, volume = {33}, number = {7}, pages = {2302--2309}, month = apr } @article{Anonymous:ADRdGI2m, title = {{Kvantemekanikk statistisk fysikk - kompendie: del 7}}, year = {2005}, pages = {1--34}, month = nov } @article{Echave:2016kl, author = {Echave, Juli{\'a}n and Spielman, Stephanie J and Wilke, Claus O}, title = {{Causes of evolutionary rate variation among protein sites}}, journal = {Nat Rev Genet}, year = {2016}, pages = {--}, month = jan } @article{Tatulian:2005ja, author = {Tatulian, Suren A and Qin, Shan and Pande, Abhay H and He, Xiaomei}, title = {{Positioning membrane proteins by novel protein engineering and biophysical approaches.}}, journal = {J. Mol. Biol.}, year = {2005}, volume = {351}, number = {5}, pages = {939--947}, month = sep } @webpage{Anonymous:rjab-QnW, title = {{Eurostat Sampling Guidelines v2 - KS-RA-08-003-EN.PDF}}, year = {2017}, month = nov, url = {message:%3C485B2AFF-B45E-4C13-A814-E57DB6E5A3C2@imr.no%3E} } @article{Alsallaq:2008bl, author = {Alsallaq, Ramzi and Zhou, Huan-Xiang}, title = {{Electrostatic rate enhancement and transient complex of protein{\textendash}protein association}}, journal = {Proteins: Struct., Funct., Bioinf.}, year = {2008}, volume = {71}, number = {1}, pages = {320--335} } @article{Hamacher:2006ej, author = {Hamacher, K and McCammon, J A}, title = {{Computing the Amino Acid Specificity of Fluctuations in Biomolecular Systems}}, journal = {J Chem Theory Comput}, year = {2006}, volume = {2}, number = {3}, pages = {873--878}, month = may } @article{Hastie:U35z2YtQ, author = {Hastie and Friedman and Tibshirani}, title = {{The Elements of Statistical Learning: Data Mining, Inference, and Prediction}} } @article{Ho:2009cq, author = {Ho, Bosco K and Agard, David A}, title = {{Probing the Flexibility of Large Conformational Changes in Protein Structures through Local Perturbations}}, journal = {PLoS Comput. Biol.}, year = {2009}, volume = {5}, number = {4}, pages = {e1000343}, month = apr } @article{Martelli:1982ty, author = {Martelli, Alberto and Montanari, Ugo}, title = {{An Efficient Unification Algorithm}}, journal = {Transactions on Programming Languages and Systems (TOPLAS}, year = {1982}, volume = {4}, number = {2}, month = apr } @article{wladmin:2014vp, author = {Katebi, Ataur and Jernigan, Robert}, title = {{Aldolase Oligomeric States are Essential for its Functional Dynamics}}, year = {2014}, pages = {1--37}, month = mar } @article{Chong:2015fp, author = {Chong, Song-Ho and Ham, Sihyun}, title = {{Thermodynamic-Ensemble Independence of Solvation Free Energy}}, journal = {J Chem Theory Comput}, year = {2015}, volume = {11}, number = {2}, pages = {378--380}, month = feb } @article{Wrabl:2010tr, author = {Wrabl, J and Hilser, V}, title = {{Investigating Homology between Proteins using Energetic Profiles}}, journal = {ncbi.nlm.nih.gov}, year = {2010} } @article{Zheng:2007bb, author = {Zheng, Wenjun and Brooks, Bernard R and Thirumalai, D}, title = {{Allosteric transitions in the chaperonin GroEL are captured by a dominant normal mode that is most robust to sequence variations}}, journal = {Biophys. J.}, year = {2007}, volume = {93}, number = {7}, pages = {2289--2299}, month = oct } @article{Aanes:2015gs, author = {Aanes, Sondre and V{\o}lstad, Jon Helge and Trenkel, Verena}, title = {{Efficient statistical estimators and sampling strategies for estimating the age composition of fish}}, journal = {Canadian Journal of Fisheries and Aquatic Sciences}, year = {2015}, volume = {72}, number = {6}, pages = {938--953}, month = jun } @article{Taylor:2007ig, author = {Taylor, William R}, title = {{Evolutionary transitions in protein fold space}}, journal = {Current Opinion in Structural Biology}, year = {2007}, volume = {17}, number = {3}, pages = {354--361} } @article{RUSSELL:1992tq, author = {Russell, RB and Barton, GJ}, title = {{Multiple protein-sequence alignment from tertiary structure comparison - assignment of global and residue confidence levels}}, journal = {Proteins}, year = {1992}, volume = {14}, number = {2}, pages = {309--323} } @article{Anonymous:u3ieYC30, title = {{small-world}}, year = {2007}, pages = {11}, month = apr } @webpage{Anonymous:eUp8RJFv, title = {{PLOS Computational Biology: The Free Energy Landscape of Dimerization of a Membrane Protein, NanC}}, url = {http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003417} } @article{Scheffer:2014jv, author = {Scheffer, M}, title = {{The forgotten half of scientific thinking}}, journal = {Proc. Natl. Acad. Sci. U. S. A.}, year = {2014}, volume = {111}, number = {17}, pages = {6119--6119}, month = apr } @article{Fan:2015dl, author = {Fan, Zhou and Dror, Ron O and Mildorf, Thomas J and Piana, Stefano and Shaw, David E}, title = {{Identifying localized changes in large systems: Change-point detection for biomolecular simulations}}, journal = {Proc. Natl. Acad. Sci. U. S. A.}, year = {2015}, volume = {112}, number = {24}, pages = {7454--7459}, month = jun } @webpage{Anonymous:kMC4GCab, title = {{Why significant variables aren{\textquoteright}t automatically good predictors}}, url = {http://www.pnas.org/content/112/45/13892.abstract.html?etoc} } @article{White:1994eu, author = {White, Stephen H and Wimley, William C}, title = {{Peptides in lipid bilayers: structural and thermodynamic basis for partitioning and folding}}, journal = {Current Opinion in Structural Biology}, year = {1994}, volume = {4}, number = {1}, pages = {79--86}, month = jan } @article{Killian:2000ta, author = {Killian, J A and von Heijne, G}, title = {{How proteins adapt to a membrane-water interface.}}, journal = {Trends in Biochemical Sciences}, year = {2000}, volume = {25}, number = {9}, pages = {429--434}, month = sep } @article{Hollup:2011ih, author = {Hollup, S M and Fuglebakk, E and Taylor, W R and Reuter, N}, title = {{Exploring the factors determining the dynamics of different protein folds}}, journal = {Protein Sci.}, year = {2011}, volume = {20}, number = {1}, pages = {197--209} } @article{Jones:2000vm, author = {Jones, S and Marin, A and Thornton, J M}, title = {{Protein domain interfaces: characterization and comparison with oligomeric protein interfaces.}}, journal = {Protein Eng.}, year = {2000}, volume = {13}, number = {2}, pages = {77--82}, month = feb } @article{Cheng:2015hw, author = {Cheng, Shanshan and Zhang, Yang and Brooks, Charles L}, title = {{PCalign: a method to quantify physicochemical similarity of protein-protein interfaces}}, journal = {BMC Bioinformatics}, year = {2015}, volume = {16}, number = {1}, pages = {3486}, month = feb } @article{Worm:2016fp, author = {Worm, Boris}, title = {{Averting a global fisheries disaster}}, journal = {Proc. Natl. Acad. Sci. U. S. A.}, year = {2016}, volume = {113}, number = {18}, pages = {4895--4897}, month = may } @article{Hinsen:2006es, author = {Hinsen, Konrad}, title = {{Comment on: ``Energy landscape of a small peptide revealed by dihedral angle principal component analysis''}}, journal = {Proteins: Struct., Funct., Bioinf.}, year = {2006}, volume = {64}, number = {3}, pages = {795--797} } @article{Sansom:2000vt, author = {Sansom, SP}, title = {{Hinges, swivels and switches: the role of prolines in signalling via transmembrane [alpha]-helices}}, journal = {Trends in pharmacological sciences}, year = {2000}, volume = {21}, number = {11}, pages = {445--451} } @article{vonBallmoos:2009tz, author = {von Ballmoos, Christoph and Wiedenmann, Alexander and Dimroth, Peter}, title = {{Essentials for ATP synthesis by F1F0 ATP synthases}}, journal = {Annu Rev Biochem}, year = {2009}, volume = {78}, pages = {649--672} } @article{Hinsen:2010ea, author = {Hinsen, Konrad}, title = {{Economic growth: indicators not targets}}, journal = {Nature}, year = {2010}, volume = {468}, number = {7326}, pages = {897--897}, month = dec } @article{Barnoud:2014fv, author = {Barnoud, Jonathan and Rossi, Giulia and Marrink, Siewert J and Monticelli, Luca}, title = {{Hydrophobic compounds reshape membrane domains.}}, journal = {PLoS Comput. Biol.}, year = {2014}, volume = {10}, number = {10}, pages = {e1003873}, month = oct } @article{CHOU:1985ut, author = {CHOU, KC}, title = {{Low-Frequency Motions in Protein Molecules Beta-Sheet and Beta-Barrel}}, journal = {Biophys. J.}, year = {1985}, volume = {48}, number = {2}, pages = {289--297} } @article{Bondi:1964un, author = {Bondi, A}, title = {{van der Waals Volumes and Radii - The Journal of Physical Chemistry (ACS Publications)}}, journal = {J. Phys. Chem.}, year = {1964} } @article{Khan:2016tk, author = {Khan, H M and He, T and Fuglebakk, E and Grauffel, C and Yang, B}, title = {{A Role for Weak Electrostatic Interactions in Peripheral Membrane Protein Binding}}, journal = {Biophysical {\ldots}}, year = {2016} } @article{GRUBMULLER:1995tu, author = {GRUBMULLER, H}, title = {{Predicting Slow Structural Transitions in Macromolecular Systems - Conformational Flooding}}, journal = {Phys. Rev. E}, year = {1995}, volume = {52}, number = {3}, pages = {2893--2906}, month = sep } @webpage{deVos:4OKoh9OH, author = {de Vos, Aart F}, title = {{primer.pdf}}, url = {http://personal.vu.nl/a.f.de.vos/primer/primer.pdf} } @incollection{MacKay:2003wf, author = {MacKay, David JC}, title = {{The sourec coding theorem}}, booktitle = {Information Thery, Inference and Learning Algorithms}, year = {2003}, pages = {66--89}, publisher = {Cambridge University Press} } @article{Amadei:1993tq, author = {Amadei, AA and Linssen, Antonius BM and Berendsen, Herman JC}, title = {{Essential Dynamics of Proteins}}, year = {1993}, volume = {17}, pages = {412--425} } @article{Schwartz:2008ia, author = {Schwartz, M A}, title = {{The importance of stupidity in scientific research}}, journal = {Journal of Cell Science}, year = {2008}, volume = {121}, number = {11}, pages = {1771--1771}, month = may } @article{Moravcevic:2012hp, author = {Moravcevic, Katarina and Oxley, Camilla L and Lemmon, Mark A}, title = {{Conditional Peripheral Membrane Proteins: Facing up to Limited Specificity}}, journal = {Structure}, year = {2012}, volume = {20}, number = {1}, pages = {15--27}, month = jan } @article{NBenTal:1997gi, author = {N Ben-Tal, B Honig C Miller S McLaughlin}, title = {{Electrostatic binding of proteins to membranes. Theoretical predictions and experimental results with charybdotoxin and phospholipid vesicles.}}, journal = {Biophys. J.}, year = {1997}, volume = {73}, number = {4}, pages = {1717--1727}, month = oct } @article{Demirel:1998ty, author = {Demirel, MC and Atilgan, AR and Jernigan, RL and Erman, B and Bahar, I}, title = {{Identification of kinetically hot residues in proteins.}}, journal = {Protein Sci.}, year = {1998}, volume = {7}, number = {12}, pages = {2522} } @article{Wust:2012ft, author = {W{\"u}st, Thomas and Landau, David P}, title = {{Optimized Wang-Landau sampling of lattice polymers: Ground state search and folding thermodynamics of HP model proteins}}, journal = {J. Chem. Phys.}, year = {2012}, volume = {137}, number = {6}, pages = {064903}, month = aug } @article{Grauffel:2012dw, author = {Grauffel, Cedric and Abboud, Ang{\`e}le and Liszczak, Glen and Marmorstein, Ronen and Arnesen, Thomas and Reuter, Nathalie}, title = {{Specificity and Versatility of Substrate Binding Sites in Four Catalytic Domains of Human N-Terminal Acetyltransferases}}, journal = {PLoS ONE}, year = {2012}, volume = {7}, number = {12}, pages = {e52642}, month = dec } @article{Sadowsky:2011hy, author = {Sadowsky, Jack D and Burlingame, Mark A and Wolan, Dennis W and McClendon, Christopher L and Jacobson, Matthew P and Wells, James A}, title = {{Turning a protein kinase on or off from a single allosteric site via disulfide trapping.}}, journal = {Proc. Natl. Acad. Sci. U. S. A.}, year = {2011}, volume = {108}, number = {15}, pages = {6056--6061}, month = apr } @article{Micheletti:2009gc, author = {Micheletti, C and Orland, H.}, title = {{MISTRAL: a tool for energy-based multiple structural alignment of proteins}}, journal = {Bioinformatics}, year = {2009}, volume = {25}, number = {20}, pages = {2663--2669}, month = oct } @article{Ochman:2000tk, author = {Ochman, H and Lawrence, JG and Groisman, EA}, title = {{Lateral gene transfer and the nature of bacterial innovation}}, journal = {Nature}, year = {2000}, volume = {405}, number = {6784}, pages = {299--304} } @article{Fuglebakk:2014gi, author = {Fuglebakk, Edvin and Tiwari, Sandhya P and Reuter, Nathalie}, title = {{Comparing the intrinsic dynamics of multiple protein structures using elastic network models.}}, journal = {Biochim. Biophys. Acta}, year = {2014}, month = sep } @article{RibasdePouplana:2001wi, author = {Ribas de Pouplana, L and Schimmel, P}, title = {{Aminoacyl-tRNA synthetases: potential markers of genetic code development}}, journal = {Trends in Biochemical Sciences}, year = {2001} } @article{Papaleo:2008vx, author = {Papaleo, E and Pasi, M and Riccardi, L and Sambi, I and Fantucci, P and Gioia, LD}, title = {{Protein flexibility in psychrophilic and mesophilic trypsins. Evidence of evolutionary conservation of protein dynamics in trypsin-like serine-proteases}}, journal = {Febs Lett}, year = {2008} } @article{HASCHEMEYER:1976wl, author = {Haschemeyer, Audrey E V}, title = {{Kinetics of protein synthesis in higher organisms in vivo}}, journal = {Trends in Biochemical Sciences}, year = {1976}, volume = {1}, number = {2}, pages = {133--136}, month = apr } @webpage{Anonymous:6M8LPMHp, title = {{Lunar phase and catch success of the striped marlin (Tetrapturus audax) in sport fishing at Los Cabos, Baja California Sur, Mexico}}, url = {http://www.scielo.sa.cr/scielo.php?pid=S0034-77442003000200026&script=sci_arttext&tlng=pt} } @article{Anonymous:vS6QApXi, title = {{matching}}, year = {2007}, pages = {10}, month = feb } @article{Aggarwal:2016jr, author = {Aggarwal, Ankush and May, Eric R and Brooks, Charles L and Klug, William S}, title = {{Nonuniform elastic properties of macromolecules and effect of prestrain on their continuum nature}}, journal = {Phys. Rev. E}, year = {2016}, volume = {93}, number = {1}, pages = {012417}, month = jan } @article{Hui:2005td, author = {Hui, S}, title = {{FlexSADRA: Flexible Structural Alignment using a Dimensionality Reduction Approach}}, journal = {University of Waterloo, Ontario, Canada}, year = {2005} } @article{Hjermann:2004fi, author = {Hjermann, D O and Ottersen, G and Stenseth, N Chr}, title = {{Competition among fishermen and fish causes the collapse of Barents Sea capelin}}, journal = {Proc Natl Acad Sci U S A}, year = {2004}, volume = {101}, number = {32}, pages = {11679--11684}, month = aug } @article{McDonald:2016fq, author = {McDonald, Sarah K and Fleming, Karen G}, title = {{Aromatic Side Chain Water-to-Lipid Transfer Free Energies Show a Depth Dependence across the Membrane Normal}}, journal = {JACS}, year = {2016}, volume = {138}, number = {25}, pages = {7946--7950}, month = jun } @article{Cullen:2008kv, author = {Cullen, Peter J}, title = {{Endosomal sorting and signalling: an emerging role for sorting nexins}}, journal = {Nat Rev Mol Cell Biol}, year = {2008}, volume = {9}, number = {7}, pages = {574--582}, month = jul } @article{Manly:1987wi, author = {Manly, Bryan and Rayner, J}, title = {{The Comparison of Sample Covariance Matrices Using Likelihood Ratio Tests}}, journal = {Biometrika}, year = {1987}, volume = {74}, number = {4}, pages = {841--847}, month = dec } @article{Redfern:2008ti, author = {Redfern, OC and Dessailly, B and Orengo, CA}, title = {{Exploring the structure and function paradigm}}, journal = {Current Opinion in Structural Biology}, year = {2008}, volume = {18}, number = {3}, pages = {394--402} } @article{Valencia:2009wi, author = {Valencia, A and Ouzounis, C and Casadio, R}, title = {{Sequence-based feature prediction and annotation of proteins}}, journal = {Genome Biology}, year = {2009} } @article{Eisenberg:1982wr, author = {Eisenberg, D and Weiss, R M and Terwilliger, T C}, title = {{The helical hydrophobic moment: a measure of the amphiphilicity of a helix.}}, journal = {Nature}, year = {1982}, volume = {299}, number = {5881}, pages = {371--374}, month = sep } @article{Hinsen:2009tn, author = {Hinsen, Konrad}, title = {{The Promises of Functional Programming}}, journal = {Computing in Science {\&} Engineering}, year = {2009}, volume = {11}, number = {4}, pages = {86--90} } @article{Ke:2005tq, author = {Ke, Runcong and Mitaku, Shigeki}, title = {{Local repulsion in protein structures as revealed by a charge distribution analysis of all amino acid sequences from the Saccharomyces cerevisiae genome}}, journal = {Journal of Physics: Condensed Matter}, year = {2005}, volume = {17}, number = {31}, pages = {S2825} } @webpage{Feynman:Yn7VjGk7, author = {Feynman, Richard P}, title = {{Cargo Cult Science}}, url = {https://www.google.no/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&cad=rja&uact=8&ved=0ahUKEwj62t_3uanNAhViM5oKHTozBU8QFggdMAA&url=http%3A%2F%2Fwww.californiachaparral.com%2Fimages%2FCargoCult.pdf&usg=AFQjCNG2FfpoiVd0OhfwzGEshrfbBZguMQ&sig2=BHxP5XTxybS8zuqK86qlZw} } @article{Wang:2005ff, author = {Wang, J}, title = {{Structural basis for ordered substrate binding and cooperativity in aspartate transcarbamoylase}}, journal = {Proc. Natl. Acad. Sci. U. S. A.}, year = {2005}, volume = {102}, number = {25}, pages = {8881--8886}, month = jun } @article{Jost:2006fr, author = {Jost, Lou}, title = {{Entropy and diversity}}, journal = {Oikos}, year = {2006}, volume = {113}, number = {2}, pages = {363--375}, month = may } @article{Perica:2014bd, author = {Perica, T and Kondo, Y and Tiwari, S P and McLaughlin, S H and Kemplen, K R and Zhang, X and Steward, A and Reuter, N and Clarke, J and Teichmann, S A}, title = {{Evolution of oligomeric state through allosteric pathways that mimic ligand binding}}, journal = {Science}, year = {2014}, volume = {346}, number = {6216}, pages = {1254346--1254346}, month = dec } @article{Sadowski:2010ju, author = {Sadowski, Michael I and Taylor, William R}, title = {{Protein structures, folds and fold spaces}}, journal = {Journal of Physics: Condensed Matter}, year = {2010}, volume = {22}, number = {3}, pages = {033103} } @article{Harris:uk, author = {Harris, Robert C and Pettitt, B Montgomery}, title = {{Effects of geometry and chemistry on hydrophobic solvation}}, journal = {pnas.org} } @article{Pontiggia:2008up, author = {Pontiggia, F and Zen, A and Micheletti, C}, title = {{Small-and Large-Scale Conformational Changes of Adenylate Kinase: A Molecular Dynamics Study of the \ldots}}, journal = {Biophys. J.}, year = {2008} } @article{Rappe:1992tb, author = {Rappe, A and Casewit, C and Colwell, K}, title = {{UFF, a full periodic table force field for molecular mechanics and molecular dynamics {\ldots}}}, journal = {JACS}, year = {1992} } @article{Link:2017dt, author = {Link, Jason S}, title = {{System-level optimal yield: increased value, less risk, improved stability, and better fisheries}}, journal = {Canadian Journal of Fisheries and Aquatic Sciences}, year = {2017}, pages = {1--16}, month = sep } @article{Marshall:1975fe, author = {Marshall, Alan G and Comisarow, Melvin B}, title = {{Fourier and Hadamard transform methods in spectroscopy}}, journal = {Anal. Chem.}, year = {1975}, volume = {47}, number = {4}, pages = {491A--504a}, month = apr } @article{Reese:1996ux, author = {Reese, M G and Lund, O and Bohr, J and Bohr, H and Hansen, J E and Brunak, S}, title = {{Distance distributions in proteins: a six-parameter representation.}}, journal = {Protein Eng.}, year = {1996}, volume = {9}, number = {9}, pages = {733--740}, month = sep } @article{Anonymous:1996ff, title = {{Phospholipases: structural and functional motifs for working at an interface.}}, journal = {FASEB J.}, year = {1996} } @article{Doruker:2000vb, author = {Doruker, P and Atilgan, AR}, title = {{Dynamics of proteins predicted by molecular dynamics simulations and analytical approaches: application to-amylase inhibitor}}, journal = {Structure}, year = {2000} } @article{Kim:2000em, author = {Kim, Suhng Wook and Quinn-Allen, Mary Ann and Camp, J Terese and Macedo-Ribeiro, Sandra and Fuentes-Prior, Pablo and Bode, Wolfram and Kane, William H}, title = {{Identification of Functionally Important Amino Acid Residues within the C2-Domain of Human Factor V Using Alanine-Scanning Mutagenesis {\dag}}}, journal = {Biochemistry}, year = {2000}, volume = {39}, number = {8}, pages = {1951--1958}, month = feb } @article{Hajjar:2007gd, author = {Hajjar, Eric and Mihajlovic, Maja and Witko-Sarsat, Veronique and Lazaridis, Themis and Reuter, Nathalie}, title = {{Computational prediction of the binding site of proteinase 3 to the plasma membrane}}, journal = {Proteins: Struct., Funct., Bioinf.}, year = {2007}, volume = {71}, number = {4}, pages = {1655--1669}, month = dec } @article{Hajjar:2009kk, author = {Hajjar, Eric and Dejaegere, Annick and Reuter, Nathalie}, title = {{Challenges in pK(a) Predictions for Proteins: The case of Asp213 in Human Proteinase 3}}, journal = {J Phys Chem A}, year = {2009}, volume = {113}, number = {43}, pages = {11783--11792} } @article{Anonymous:-ZfHWARk, title = {{Efficient Estimators of Abundance, for Fish and Plankton SurveysAuthor(s): Michael PenningtonSource: Biometrics, Vol. 39, No. 1 (Mar., 1983), pp. 281-286Published by:}}, year = {2010}, pages = {1--7}, month = may } @article{Dalziel:2008hg, author = {Dalziel, Benjamin D and Morales, Juan M and Fryxell, John M}, title = {{Fitting Probability Distributions to Animal Movement Trajectories: Using Artificial Neural Networks to Link Distance, Resources, and Memory}}, journal = {Am Nat}, year = {2008}, volume = {172}, number = {2}, pages = {248--258}, month = aug } @article{Aherne:1998wm, author = {Aherne, FJ and Thacker, NA and Rockett, PI}, title = {{The Bhattacharyya metric as an absolute similarity measure for frequency coded data}}, journal = {Kybernetika}, year = {1998}, volume = {34}, number = {4}, pages = {363--368} } @article{Hirst:2005bt, author = {Hirst, David and Storvik, Geir and Aldrin, Magne and Aanes, Sondre and Huseby, Ragnar Bang}, title = {{Estimating catch-at-age by combining data from different sources}}, journal = {Canadian Journal of Fisheries and Aquatic Sciences}, year = {2005}, month = jul } @article{Hinsen:2018fg, author = {Hinsen, Konrad}, title = {{Digital scientific notations as a human-computer interface in computer-aided research}}, year = {2018}, month = mar } @article{Fornasari:2007by, author = {Fornasari, Mar{\'\i}a Silvina and Parisi, Gustavo and Echave, Juli{\'a}n}, title = {{Quaternary structure constraints on evolutionary sequence divergence.}}, journal = {Molecular Biology and Evolution}, year = {2007}, volume = {24}, number = {2}, pages = {349--351}, month = feb } @article{Petersen:2008up, author = {Petersen, Kaare Brandt and Pedersen, Michael Syskind}, title = {{The Matrix Cookbook}}, year = {2008}, pages = {1--71}, month = nov } @article{Laughlin:2000vt, author = {Laughlin, RB and Pines, D}, title = {{The theory of everything}}, journal = {Proc. Natl. Acad. Sci. U. S. A.}, year = {2000}, volume = {97}, number = {1}, pages = {28} } @article{Wimley:1993eu, author = {Wimley, William C and White, Stephen H}, title = {{Membrane partitioning: Distinguishing bilayer effects from the hydrophobic effect}}, journal = {Biochemistry}, year = {1993}, volume = {32}, number = {25}, pages = {6307--6312}, month = jun } @article{Kamerlin:2010ei, author = {Kamerlin, Shina C L and Warshel, Arieh}, title = {{Reply to Karplus: Conformational dynamics have no role in the chemical step}}, journal = {Proc Natl Acad Sci U S A}, year = {2010}, volume = {107}, number = {17}, pages = {E72--E72}, month = apr } @article{Isaksen:2014gz, author = {Isaksen, Geir Villy and Aqvist, Johan and Brandsdal, Bj{\o}rn Olav}, title = {{Protein Surface Softness Is the Origin of Enzyme Cold-Adaptation of Trypsin.}}, journal = {PLoS Comput. Biol.}, year = {2014}, volume = {10}, number = {8}, pages = {e1003813}, month = aug } @article{Kantrowitz:1988fn, author = {Kantrowitz, E and Lipscomb, W}, title = {{Escherichia coli aspartate transcarbamylase: the relation between structure and function}}, journal = {Science}, year = {1988}, volume = {241}, number = {4866}, pages = {669--674}, month = aug } @article{Cheetham:2001tq, author = {Cheetham, J J and Hilfiker, S and Benfenati, F and Weber, T and Greengard, P and Czernik, A J}, title = {{Identification of synapsin I peptides that insert into lipid membranes.}}, journal = {Biochem J}, year = {2001}, volume = {354}, number = {Pt 1}, pages = {57--66}, month = feb } @article{vonHeijne:_f_JVKXt, author = {von Heijne, Gunnar}, title = {{Formation of Transmembrane Helices In Vivo{\textemdash}Is Hydrophobicity All that Matters?}}, journal = {jgp.rupress.org} } @article{Borenstein:2008um, author = {Borenstein, E and Kupiec, M and Feldman, MW and Ruppin, E}, title = {{Large-scale reconstruction and phylogenetic analysis of metabolic environments}}, journal = {Proc. Natl. Acad. Sci. U. S. A.}, year = {2008}, volume = {105}, number = {38}, pages = {14482} } @article{Kitao:1994wf, author = {Kitao, A and Hayward, S and GO, N}, title = {{Comparison of Normal-Mode Analyses on a Small Globular Protein in Dihedral Angle Space and Cartesian Coordinate Space}}, journal = {Biophys. Chem.}, year = {1994}, volume = {52}, number = {2}, pages = {107--114} } @article{Kohannim:2013jz, author = {Kohannim, S and Iwasaki, T}, title = {{24430125}}, journal = {Journal of the Royal Society, Interface / the Royal Society}, year = {2013}, volume = {11}, number = {92}, pages = {20131073--20131073}, month = dec } @article{Anonymous:kg5fk2pg, title = {{M7CL Editor Owners Manual}}, year = {2005}, pages = {1--72}, month = aug } @article{Capozzi:2007db, author = {Capozzi, Francesco and Luchinat, Claudio and Micheletti, Cristian and Pontiggia, Francesco}, title = {{Essential dynamics of helices provide a functional classification of EF-hand proteins}}, journal = {J Proteome Res}, year = {2007}, volume = {6}, number = {11}, pages = {4245--4255} } @article{Shih:2012cv, author = {Shih, Chien-Hua and Chang, Chih-Min and Lin, Yeong-Shin and Lo, Wei-Cheng and Hwang, Jenn-Kang}, title = {{Evolutionary information hidden in a single protein structure}}, journal = {Proteins: Struct., Funct., Bioinf.}, year = {2012}, volume = {80}, number = {6}, pages = {1647--1657}, month = mar } @article{Chennubhotla:2005bb, author = {Chennubhotla, Chakra and Rader, A J and Yang, Lee-Wei and Bahar, Ivet}, title = {{Elastic network models for understanding biomolecular machinery: from enzymes to supramolecular assemblies.}}, journal = {Phys. Biol.}, year = {2005}, volume = {2}, number = {4}, pages = {S173--S180}, month = nov } @article{Harrison:1997ex, author = {Harrison, Paul M and Bamborough, Paul and Daggett, Valerie and Prusiner, Stanley B and Cohen, Fred E}, title = {{The prion folding problem}}, journal = {Current Opinion in Structural Biology}, year = {1997}, volume = {7}, number = {1}, pages = {53--59}, month = feb } @article{Robic:2009dv, author = {Robic, Srebrenka}, title = {{Mathematics, thermodynamics, and modeling to address ten common misconceptions about protein structure, folding, and stability.}}, journal = {CBE Life Sci Educ}, year = {2009}, volume = {9}, number = {3}, pages = {189--195}, month = dec } @article{Quemeneur:2014eq, author = {Quemeneur, Fran{\c c}ois and Sigurdsson, Jon K and Renner, Marianne and Atzberger, Paul J and Bassereau, Patricia and Lacoste, David}, title = {{Shape matters in protein mobility within membranes}}, journal = {Proc. Natl. Acad. Sci. U. S. A.}, year = {2014}, volume = {111}, number = {14}, pages = {5083--5087}, month = apr } @article{Moler:2008td, author = {Moler, Cleve}, title = {{Numerical Computing with MATLAB. Chapter 8: Fourier Analysis}}, year = {2008}, pages = {1--21}, month = feb } @article{Mizuno:2014dz, author = {Mizuno, Hideyuki and Mossa, Stefano and Barrat, Jean-Louis}, title = {{Acoustic excitations and elastic heterogeneities in disordered solids}}, journal = {Proc. Natl. Acad. Sci. U. S. A.}, year = {2014}, volume = {111}, number = {33}, pages = {11949--11954}, month = aug } @article{Nowakowski:2011bp, author = {Nowakowski, Piotr and Ciepiela, Eryk and Har{\k{e}}{\.{z}}lak, Daniel and Kocot, Joanna and Kasztelnik, Marek and Barty{\'{n}}ski, Tomasz and Meizner, Jan and Dyk, Grzegorz and Malawski, Maciej}, title = {{The Collage Authoring Environment}}, journal = {Procedia Computer Science}, year = {2011}, volume = {4}, pages = {608--617}, month = jan } @article{Shaw:2005cn, author = {Shaw, DE}, title = {{A fast, scalable method for the parallel evaluation of distance-limited pairwise particle interactions}}, journal = {J. Comput. Chem.}, year = {2005}, volume = {26}, number = {13}, pages = {1318--1328} } @article{Sierk:2004ef, author = {Sierk, ML and Pearson, WR}, title = {{Sensitivity and selectivity in protein structure comparison}}, journal = {Protein Sci.}, year = {2004}, volume = {13}, number = {3}, pages = {773--785} } @article{Spencer:1999df, author = {Spencer, A G and Thuresson, E and Otto, J C and Song, I and Smith, T and DeWitt, D L and Garavito, R M and Smith, W L}, title = {{The Membrane Binding Domains of Prostaglandin Endoperoxide H Synthases 1 and 2: PEPTIDE MAPPING AND MUTATIONAL ANALYSIS}}, journal = {J. Biol. Chem.}, year = {1999}, volume = {274}, number = {46}, pages = {32936--32942}, month = nov } @article{Wimley:1996vp, author = {Wimley, W C and White, S H}, title = {{Experimentally determined hydrophobicity scale for proteins at membrane interfaces}}, journal = {Nat. Struct Biol.}, year = {1996} } @article{Hinsen:jw, author = {Hinsen, Konrad}, title = {{Daydreaming about Scientific Programming}}, journal = {Computing in Science {\&} Engineering}, volume = {15}, number = {5}, pages = {77--79} } @article{Singh:2011ci, author = {Singh, Gurpreet and Tieleman, D Peter}, title = {{Using the Wimley{\textendash}White Hydrophobicity Scale as a Direct Quantitative Test of Force Fields: The MARTINI Coarse-Grained Model}}, journal = {J Chem Theory Comput}, year = {2011}, volume = {7}, number = {7}, pages = {2316--2324}, month = jul } @article{Kalli:2014wl, author = {Kalli, A C and Sansom, MSP}, title = {{Interactions of peripheral proteins with model membranes as viewed by molecular dynamics simulations}}, journal = {Biochem. Soc. Trans.}, year = {2014} } @article{Lomize:2011iz, author = {Lomize, M A and Pogozheva, I D and Joo, H and Mosberg, H I and Lomize, A L}, title = {{OPM database and PPM web server: resources for positioning of proteins in membranes}}, journal = {Nucleic Acids Res.}, year = {2011}, volume = {40}, number = {D1}, pages = {D370--D376}, month = dec } @article{Laio:2008iw, author = {Laio, Alessandro and Gervasio, Francesco L}, title = {{Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science}}, journal = {Rep. Prog. Phys.}, year = {2008}, volume = {71}, number = {12}, pages = {126601}, month = nov } @article{Hess:2002ve, author = {Hess, Berk}, title = {{Convergence of sampling in protein simulations.}}, journal = {Phys Rev E Stat Nonlin Soft Matter Phys}, year = {2002}, volume = {65}, number = {3 Pt 1}, pages = {031910}, month = mar } @article{Yang:2008wr, author = {Yang, L and Chng, C}, title = {{Coarse-grained models reveal functional dynamics-I. elastic network models--theories, \ldots}}, journal = {Bioinformatics and Biology Insights}, year = {2008} } @article{KURTWUTHRICH:2002tm, author = {KURTW{\"U}THRICH}, title = {{NMR STUDIES OF STRUCTURE AND FUNCTION OF BIOLOGICAL MACROMOLECULES}}, journal = {Nobel Lecture}, year = {2002}, pages = {1--33} } @article{Kim:2005cd, author = {Kim, Moon K and Jernigan, Robert L and Chirikjian, Gregory S}, title = {{Rigid-cluster models of conformational transitions in macromolecular machines and assemblies.}}, journal = {Biophysj}, year = {2005}, volume = {89}, number = {1}, pages = {43--55}, month = jul } @article{McLeish:2015ez, author = {McLeish, Tom C B and Cann, Martin J and Rodgers, Thomas L}, title = {{Dynamic Transmission of Protein Allostery without Structural Change: Spatial Pathways or Global Modes?}}, journal = {Biophysj}, year = {2015}, volume = {109}, number = {6}, pages = {1240--1250}, month = sep } @article{Echave:2009ww, author = {Echave, Julian}, title = {{On the similarity of protein motions}}, year = {2009}, pages = {1--9}, month = dec } @article{Kim:2015bf, author = {Kim, Hanseong and Zou, Taisong and Modi, Chintan and D{\"o}rner, Katerina and Grunkemeyer, Timothy J and Chen, Liqing and Fromme, Raimund and Matz, Mikhail V and Ozkan, S Banu and Wachter, Rebekka M}, title = {{A Hinge Migration Mechanism Unlocks the Evolution of Green-to-Red Photoconversion in GFP-like Proteins}}, journal = {Structure}, year = {2015}, volume = {23}, number = {1}, pages = {34--43}, month = jan } @article{Marsh:2008hj, author = {Marsh, Derek}, title = {{Protein modulation of lipids, and vice-versa, in membranes.}}, journal = {Biochim. Biophys. Acta}, year = {2008}, volume = {1778}, number = {7-8}, pages = {1545--1575}, month = jul } @article{Chen:2006jh, author = {Chen, Changjun and Li, Lin and Xiao, Yi}, title = {{Identification of key residues in proteins by using their physical characters}}, journal = {Phys. Rev. E}, year = {2006}, volume = {73}, number = {4}, pages = {7}, month = apr } @article{Hollup:2005fc, author = {Hollup, SM and Salensminde, G and Reuter, N}, title = {{WEBnm@: a web application for normal mode analyses of proteins}}, journal = {BMC Bioinformatics}, year = {2005}, volume = {6}, pages = {52} } @article{Kutateladze:2001ir, author = {Kutateladze, T}, title = {{Structural Mechanism of Endosome Docking by the FYVE Domain}}, journal = {Science}, year = {2001}, volume = {291}, number = {5509}, pages = {1793--1796}, month = mar } @article{Radkiewicz:2001vz, author = {Radkiewicz, J L JL and Zipse, H H and Clarke, S S and Houk, K N KN}, title = {{Neighboring side chain effects on asparaginyl and aspartyl degradation: an ab initio study of the relationship between peptide conformation and backbone NH acidity.}}, journal = {JACS}, year = {2001}, volume = {123}, number = {15}, pages = {3499--3506}, month = apr } @book{Anonymous:2005ta, publisher = {Elsevier}, year = {2005} } @article{Wells:2007uo, author = {Wells, JA and McClendon, CL}, title = {{Reaching for high-hanging fruit in drug discovery at protein{\textendash}protein interfaces}}, journal = {Nature}, year = {2007}, volume = {450}, number = {7172}, pages = {1001--1009} } @article{Maguid:2006fg, author = {Maguid, Sandra and Fern{\'a}ndez-Alberti, Sebasti{\'a}n and Parisi, Gustavo and Echave, Juli{\'a}n}, title = {{Evolutionary conservation of protein backbone flexibility}}, journal = {Journal of Molecular Evolution}, year = {2006}, volume = {63}, number = {4}, pages = {448--457}, month = oct } @article{Eidhammer:2000tx, author = {Eidhammer, Ingvar and Jonassen, Inge and Taylor, William R}, title = {{Structure Comparison and Structure Patterns}}, journal = {J Comput Biol}, year = {2000}, volume = {7}, number = {5}, pages = {685--716}, month = oct } @article{Hendrickson:2000wa, author = {Hendrickson, W A}, title = {{Synchrotron crystallography.}}, journal = {Trends in Biochemical Sciences}, year = {2000}, volume = {25}, number = {12}, pages = {637--643}, month = dec } @article{Levy:2010uj, author = {Levy, Emmanuel D and Gelly, Jean-Christophe and Baaden, Marc}, title = {{Collective motions conserved at nanosecond and evolutionary timescales reveal mobile regions in proteins -unpublished}}, year = {2010}, pages = {1--22}, month = jun } @article{Sanejouand:f_1THCXW, author = {Sanejouand, Y-H}, title = {{Elastic Network Models: Theoretical and Empirical Foundations}} } @article{Arendt:2008hj, author = {Arendt, J and Reznick, D}, title = {{Convergence and parallelism reconsidered: what have we learned about the genetics of adaptation?}}, journal = {Trends in Ecology {\&} Evolution}, year = {2008}, volume = {23}, number = {1}, pages = {26--32} } @article{Agasoster:2003bja, author = {Agas{\o}ster, Armelle Varnier and Halskau, {\O}yvind and Fuglebakk, Edvin and Fr{\o}ystein, Nils Age and Muga, Arturo and Holmsen, Holm and Martinez, Aurora}, title = {{The interaction of peripheral proteins and membranes studied with alpha-lactalbumin and phospholipid bilayers of various compositions.}}, journal = {J. Biol. Chem.}, year = {2003}, volume = {278}, number = {24}, pages = {21790--21797}, month = jun } @article{Anonymous:vr2dt-Sw, title = {{ess}}, year = {2007}, pages = {3} } @article{Yang:2008wr, author = {Yang, L and Chng, C}, title = {{Coarse-grained models reveal functional dynamics-I. elastic network models{\textendash}theories, {\ldots}}}, journal = {Bioinformatics and Biology Insights}, year = {2008} } @article{Li:2009gx, author = {Li, Da-Wei and BrUschweiler, Rafael}, title = {{All-Atom Contact Model for Understanding Protein Dynamics from Crystallographic B-Factors}}, journal = {Biophysj}, year = {2009}, volume = {96}, number = {8}, pages = {3074--3081}, month = apr } @article{Karplus:2010de, author = {Karplus, Martin}, title = {{Role of conformation transitions in adenylate kinase}}, journal = {Proc. Natl. Acad. Sci. U. S. A.}, year = {2010}, volume = {107}, number = {17}, pages = {E71--E71} } @article{Bray:2011cd, author = {Bray, Jenelle K and Weiss, Dahlia R and Levitt, Michael}, title = {{Optimized Torsion-Angle Normal Modes Reproduce Conformational Changes More Accurately Than Cartesian Modes}}, journal = {Biophys. J.}, year = {2011}, volume = {101}, number = {12}, pages = {2966--2969}, month = dec } @article{Valadie:2003jd, author = {Valadi{\'e}, H and Lacap{\v c}re, J J and Sanejouand, Y-H and Etchebest, C}, title = {{Dynamical Properties of the MscL of Escherichia coli: A Normal Mode Analysis}}, journal = {J. Mol. Biol.}, year = {2003}, volume = {332}, number = {3}, pages = {657--674}, month = sep } @article{Taylor:2002ep, author = {Taylor, William R}, title = {{A 'periodic table' for protein structures.}}, journal = {Nature}, year = {2002}, volume = {416}, number = {6881}, pages = {657--660}, month = apr } @webpage{Anonymous:rsO8kZJW, title = {{Phys. Rev. Lett. 113, 148101 (2014) - Mechanosensitive Channel Activation by Diffusio-Osmotic Force}}, url = {http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.113.148101} } @article{Bjorge:2002tk, author = {Bj{\o}rge, Kjell Magnar}, title = {{Grunnleggende lydteknikk for PA lydtekniker}}, year = {2002}, pages = {1--19}, month = oct } @article{CHOE:2007jg, author = {CHOE, S and SUN, S}, title = {{Bending Elasticity of Anti-Parallel $\beta$-Sheets}}, journal = {Biophys. J.}, year = {2007}, volume = {92}, number = {4}, pages = {1204--1214}, month = feb } @webpage{Anonymous:_PvphxHB, title = {{Eppur Si Muove! The 2013 Nobel Prize in Chemistry}}, url = {http://www.sciencedirect.com/science/article/pii/S0969212613004395} } @article{Yang:2007td, author = {Yang, L and Song, G and Jernigan, RL}, title = {{How well can we understand large-scale protein motions using normal modes of elastic network models?}}, journal = {Biophys. J.}, year = {2007}, volume = {93}, number = {3}, pages = {920--929} } @article{Khatib:2011hp, author = {Khatib, Firas and DiMaio, Frank and Cooper, Seth and Kazmierczyk, Maciej and Gilski, Miroslaw and Krzywda, Szymon and Zabranska, Helena and Pichova, Iva and Thompson, James and Popovi{\'c}, Zoran and Jaskolski, Mariusz and Baker, David}, title = {{Crystal structure of a monomeric retroviral protease solved by protein folding game players}}, journal = {Nature Structural {\&} Molecular Biology}, year = {2011}, volume = {18}, number = {10}, pages = {1175--1177}, month = sep } @article{Malhotra:2015jy, author = {Malhotra, Sony and Mathew, Oommen K and Sowdhamini, Ramanathan}, title = {{DOCKSCORE: a webserver for ranking protein-protein docked poses}}, journal = {BMC Bioinformatics}, year = {2015}, volume = {16}, number = {1}, pages = {13}, month = apr } @article{King:1969to, author = {King, J L and Jukes, T H}, title = {{Non-Darwinian evolution.}}, journal = {Science}, year = {1969}, volume = {164}, number = {3881}, pages = {788--798}, month = may } @article{Wintrode:2000jv, author = {Wintrode, P L and Miyazaki, K and Arnold, F H}, title = {{Cold adaptation of a mesophilic subtilisin-like protease by laboratory evolution.}}, journal = {J. Biol. Chem.}, year = {2000}, volume = {275}, number = {41}, pages = {31635--31640}, month = oct } @article{Fuglebakk:2012enb, author = {Fuglebakk, E and Echave, J and Reuter, N}, title = {{Measuring and comparing structural fluctuation patterns in large protein datasets}}, journal = {Bioinformatics}, year = {2012}, volume = {28}, number = {19}, pages = {2431--2440}, month = sep } @article{Frazier:2002we, author = {Frazier, April A and Wisner, Mark A and Malmberg, Nathan J and Victor, Kenneth G and Fanucci, Gail E and Nalefski, Eric A and Falke, Joseph J and Cafiso, David S}, title = {{Membrane orientation and position of the C2 domain from cPLA2 by site-directed spin labeling.}}, journal = {Biochemistry}, year = {2002}, volume = {41}, number = {20}, pages = {6282--6292}, month = may } @article{Baldwin:2016bh, author = {Baldwin, Robert L and Rose, George D}, title = {{How the hydrophobic factor drives protein folding.}}, journal = {Proc. Natl. Acad. Sci. U. S. A.}, year = {2016}, volume = {113}, number = {44}, pages = {12462--12466}, month = nov } @article{Hill:1996ub, author = {Hill, C P and Worthylake, D and Bancroft, D P and Christensen, A M and Sundquist, W I}, title = {{Crystal structures of the trimeric human immunodeficiency virus type 1 matrix protein: implications for membrane association and assembly}}, journal = {Proceedings of the {\ldots}}, year = {1996} } @article{Schafer:2011fd, author = {Sch{\"a}fer, Lars V and de Jong, Djurre H and Holt, Andrea and Rzepiela, Andrzej J and de Vries, Alex H and Poolman, Bert and Killian, J Antoinette and Marrink, Siewert J}, title = {{Lipid packing drives the segregation of transmembrane helices into disordered lipid domains in model membranes}}, journal = {Proc Natl Acad Sci U S A}, year = {2011}, volume = {108}, number = {4}, pages = {1343--1348} } @article{Mitternacht:2011eo, author = {Mitternacht, Simon and Berezovsky, Igor N.}, title = {{Binding leverage as a molecular basis for allosteric regulation}}, journal = {PLoS Comput. Biol.}, year = {2011}, volume = {7}, number = {9}, pages = {e1002148} } @webpage{Anonymous:nIB5nxqp, title = {{Phys. Rev. Lett. 114, 098101 (2015) - Membrane Composition Variation and Underdamped Mechanics near Transmembrane Proteins and Coats}}, url = {http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.114.098101} } @webpage{Anonymous:haR406fp, title = {{Prot_dyn_fancy.pdf}}, url = {http://dirac.cnrs-orleans.fr/~piazza/PB/files/Prot_dyn_fancy.pdf} } @article{Ruepp:2009di, author = {Ruepp, A and Waegele, B and Lechner, M and Brauner, B and Dunger-Kaltenbach, I and Fobo, G and Frishman, G and Montrone, C and Mewes, H W}, title = {{CORUM: the comprehensive resource of mammalian protein complexes--2009}}, journal = {Nucleic Acids Res.}, year = {2009}, volume = {38}, number = {Database}, pages = {D497--D501}, month = dec } @article{Isaksen:tl, author = {Isaksen, Geir Villy and Aqvist, Johan and Brandsdal, Bj{\o}rn Olav}, title = {{Enzyme surface rigidity tunes the temperature dependence of catalytic rates}}, journal = {pnas.org} } @article{Iversen:2002fj, author = {Iversen, Hege and Fuglebakk, Edvin and Holmsen, Holm and Fukami, Miriam H}, title = {{Identification of minor metabolites of phospholipid signal molecules in [(32)P]P(i)-labelled platelets.}}, journal = {Platelets}, year = {2002}, volume = {13}, number = {5-6}, pages = {279--284}, month = jul } @article{Raimondi:2010em, author = {Raimondi, Francesco and Orozco, Modesto and Fanelli, Francesca}, title = {{Deciphering the deformation modes associated with function retention and specialization in members of the Ras superfamily}}, journal = {Structure}, year = {2010}, volume = {18}, number = {3}, pages = {402--414} } @article{Popovych:2006js, author = {Popovych, Nataliya and Sun, Shangjin and Ebright, Richard H and Kalodimos, Charalampos G}, title = {{Dynamically driven protein allostery.}}, journal = {Nature Structural {\&} Molecular Biology}, year = {2006}, volume = {13}, number = {9}, pages = {831--838}, month = sep } @article{Huang:2014dp, author = {Huang, Rick K and Baxa, Ulrich and Aldrian, Gudrun and Ahmed, Abdullah B and Wall, Joseph S and Mizuno, Naoko and Antzutkin, Oleg and Steven, Alasdair C and Kajava, Andrey V}, title = {{Conformational Switching in PolyGln Amyloid Fibrils Resulting from a Single Amino Acid Insertion}}, journal = {Biophys. J.}, year = {2014}, volume = {106}, number = {10}, pages = {2134--2142}, month = may } @article{Lathrop:2001wu, author = {Lathrop, B and Gadd, M and Biltonen, R L and Rule, G S}, title = {{Changes in Ca2+ affinity upon activation of Agkistrodon piscivorus piscivorus phospholipase A2.}}, journal = {Biochemistry}, year = {2001}, volume = {40}, number = {11}, pages = {3264--3272}, month = mar } @article{Skjaerven:2015fr, author = {Skjaerven, Lars and Cuellar, Jorge and Martinez, Aurora and Valpuesta, Jos{\'e} Mar{\'\i}a}, title = {{Dynamics, flexibility, and allostery in molecular chaperonins}}, journal = {Febs Lett}, year = {2015}, month = jun } @article{Hayward:1997vf, author = {Hayward, Steven and Kitao, Akio and Berendsen, Herman JC}, title = {{Model-free methods of analyzing domain motions in proteins from simulation: A comparison of normal mode analysis and molecular dynamics simulation of lysozyme}}, journal = {Proteins: Struct., Funct., Bioinf.}, year = {1997}, volume = {27}, number = {3}, pages = {425--437} } @article{Tiberti:2015hy, author = {Tiberti, Matteo and Invernizzi, Gaetano and Papaleo, Elena}, title = {{A (dis)similarity index to compare correlated motions in molecular simulations}}, journal = {J Chem Theory Comput}, year = {2015}, pages = {150817160752008}, month = aug } @article{Bandeira:2016fc, author = {Bandeira, Afonso S}, title = {{Inference on graphs via semidefinite programming}}, journal = {Proc. Natl. Acad. Sci. U. S. A.}, year = {2016}, volume = {113}, number = {16}, pages = {4238--4239}, month = apr } @article{Johnston:2014kp, author = {Johnston, Iain G and Rickett, Benjamin C and Jones, Nick S}, title = {{Explicit Tracking of Uncertainty Increases the Power of Quantitative Rule-of-Thumb Reasoning in Cell Biology}}, journal = {Biophys. J.}, year = {2014}, volume = {107}, number = {11}, pages = {2612--2617}, month = dec } @article{Karplus:2011jt, author = {Karplus, Martin}, title = {{Behind the folding funnel diagram.}}, journal = {Nat Chem Biol}, year = {2011}, volume = {7}, number = {7}, pages = {401--404}, month = jul } @inproceedings{Lee:2011un, author = {Lee, Ken Yoong and Bretschneider, Timo Rolf}, title = {{Derivation of separability measures based on central complex Gaussian and Wishart distributions}}, booktitle = {Geoscience and Remote Sensing Symposium (IGARSS), 2011 IEEE International}, year = {2011}, pages = {3740--3743}, publisher = {IEEE} } @article{Latchman:1997vu, author = {Latchman, D S}, title = {{ScienceDirect.com - The International Journal of Biochemistry {\&} Cell Biology - Transcription factors: An overview}}, journal = {The international journal of biochemistry {\&} cell biology}, year = {1997} } @webpage{Anonymous:8ha0z405, title = {{PLOS Computational Biology: Are Current Atomistic Force Fields Accurate Enough to Study Proteins in Crowded Environments?}}, url = {http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003638;jsessionid=7E840D2A56A724EEF19BED6EA01B786C} } @article{Hinsen:2016ui, author = {Hinsen, K}, title = {{The Power to Create Chaos}}, journal = {Computing in Science {\&} Engineering}, year = {2016} } @article{Kohn:2008ug, author = {Kohn, M}, title = {{Darwin 200: The needs of the many.}}, journal = {Nature}, year = {2008}, volume = {456}, number = {7220}, pages = {296} } @article{Grauffel:2013uf, author = {Grauffel, Cedric and Yang, Boqian and He, Tao and Roberts, Mary F and Gershenson, Anne and Reuter, Nathalie}, title = {{Cation{\textminus}$\pi$ Interactions As Lipid-Specific Anchors for Phosphatidylinositol-Specific Phospholipase C}}, journal = {Journal of the {\ldots}}, year = {2013} } @article{Jao:2004dx, author = {Jao, Christine C and Der-Sarkissian, Ani and Chen, Jeannie and Langen, Ralf}, title = {{Structure of membrane-bound alpha-synuclein studied by site-directed spin labeling.}}, journal = {Proc Natl Acad Sci U S A}, year = {2004}, volume = {101}, number = {22}, pages = {8331--8336}, month = jun } @article{Skjaerven:2011ik, author = {Skjaerven, Lars and Grant, Barry and Muga, Arturo and Teigen, Knut and McCammon, J Andrew and Reuter, Nathalie and Martinez, Aurora}, title = {{Conformational sampling and nucleotide-dependent transitions of the GroEL subunit probed by unbiased molecular dynamics simulations.}}, journal = {PLoS Comput. Biol.}, year = {2011}, volume = {7}, number = {3}, pages = {e1002004}, month = mar } @article{Hinsen:bp, author = {Hinsen, Konrad and L{\"a}ufer, Konstantin and Thiruvathukal, George K}, title = {{Essential Tools: Version Control Systems}}, journal = {Computing in Science {\&} Engineering}, volume = {11}, number = {6}, pages = {84--91} } @article{Yang:2008vb, author = {Yang, Lei and Song, Guang and Carriquiry, Alicia and Jernigan, Robert L}, title = {{Close correspondence between the motions from principal component analysis of multiple HIV-1 protease structures and elastic network modes}}, journal = {Structure}, year = {2008}, volume = {16}, number = {2}, pages = {321--330} } @article{Halle:2004hu, author = {Halle, B}, title = {{Biomolecular cryocrystallography: Structural changes during flash-cooling}}, journal = {Proc. Natl. Acad. Sci. U. S. A.}, year = {2004}, volume = {101}, number = {14}, pages = {4793--4798}, month = mar } @article{Song:2006vc, author = {Song, G and Jernigan, RL}, title = {{An enhanced elastic network model to represent the motions of domain-swapped proteins}}, journal = {Proteins: Struct., Funct., Bioinf.}, year = {2006}, volume = {63}, number = {1}, pages = {197--209} } @article{Hand:2001us, author = {Hand, DJ and Till, RJ}, title = {{A simple generalisation of the area under the ROC curve for multiple class classification problems}}, journal = {Machine Learning}, year = {2001}, volume = {45}, number = {2}, pages = {171--186} } @article{Fealey:2012jq, author = {Fealey, Michael E and Gauer, Jacob W and Kempka, Sarah C and Miller, Katie and Nayak, Kamakshi and Sutton, R Bryan and Hinderliter, Anne}, title = {{Negative Coupling as a Mechanism for Signal Propagation between C2 Domains of Synaptotagmin I}}, journal = {PLoS ONE}, year = {2012}, volume = {7}, number = {10}, pages = {e46748}, month = oct } @article{Kneller:2008cv, author = {Kneller, G R and Hinsen, K and Sutmann, G and Calandrini, V}, title = {{Scaling laws and memory effects in the dynamics of liquids and proteins}}, journal = {Phys. Part. Nuclei Lett.}, year = {2008}, volume = {5}, number = {3}, pages = {189--195}, month = jun } @article{Ichiye:1991db, author = {Ichiye, T and Karplus, M}, title = {{Collective motions in proteins: a covariance analysis of atomic fluctuations in molecular dynamics and normal mode simulations.}}, journal = {Proteins: Struct., Funct., Bioinf.}, year = {1991}, volume = {11}, number = {3}, pages = {205--217} } @article{Mitternacht:2011to, author = {Mitternacht, Simon and Berezovsky, Igor N.}, title = {{On the importance of amino acid sequence and spatial proximity of interacting residues for protein folding.}}, journal = {J Biomol Struct Dyn}, year = {2011}, volume = {28}, number = {4}, pages = {607--9; discussion 669--674}, month = feb } @article{vonHeijne:1999tq, author = {von Heijne, G}, title = {{A day in the life of Dr K. or how I learned to stop worrying and love lysozyme: A tragedy in six acts}}, journal = {J. Mol. Biol.}, year = {1999}, volume = {293}, number = {2}, pages = {367--379} } @article{Ishima:2000vt, author = {Ishima, R and Torchia, DA}, title = {{Protein dynamics from NMR}}, journal = {Nature Structural {\&} Molecular Biology}, year = {2000}, volume = {7}, number = {9}, pages = {740--743} } @webpage{Tufte:vw, author = {Tufte, Edvard R}, title = {{The Visual Display of Quantitative Information}}, url = {http://sciencepolicy.colorado.edu/students/envs_5120/tufte_2001.pdf} } @article{Przytycka:2005ws, author = {Przytycka, Teresa and Davis, George and Song, Nan and Durand, Dannie}, title = {{Graph Theoretical Insights into Evolution of Multidomain Proteins}}, year = {2005}, pages = {1--15}, month = mar } @article{Berman:2003wd, author = {Berman, H and Henrick, K and Nakamura, Haruki}, title = {{Announcing the worldwide protein data bank}}, journal = {Nat. Struct Biol.}, year = {2003} } @article{Science:2009vr, author = {Science, American Association for the Advancement of}, title = {{Science Magazine}}, year = {2009}, pages = {1--2}, month = jul } @article{Bohrnstedt:1969ud, author = {Bohrnstedt, George W and Goldberger, Arthur S}, title = {{On the Exact Covariance of Products of Random Variables}}, journal = {Journal of the American Statistical Association}, year = {1969}, volume = {64}, number = {328}, pages = {1439--1442}, month = dec } @article{Doets:2011vo, author = {Doets, Kees and Eijck, Jan van}, title = {{The Haskell Road to Logic, Math and Programming}}, year = {2011}, pages = {1--449} } @article{Hanley:1982te, author = {Hanley, James A. and McNeil, Barbera J.}, title = {{The meaning and use of the area under a receiver operating characteristic (ROC) curve.}}, journal = {Radiology}, year = {1982}, volume = {143}, number = {1}, pages = {29--36}, month = apr } @article{Carugo:2001gk, author = {Carugo, O}, title = {{A normalized root-mean-spuare distance for comparing protein three-dimensional structures}}, journal = {Protein Sci.}, year = {2001}, volume = {10}, number = {7}, pages = {1470--1473}, month = jul } @article{Fang:2012cd, author = {Fang, Ferric C and Steen, R Grant and Casadevall, Arturo}, title = {{Misconduct accounts for the majority of retracted scientific publications}}, journal = {Proc. Natl. Acad. Sci. U. S. A.}, year = {2012}, volume = {109}, number = {42}, pages = {17028--17033}, month = oct } @article{Cisneros:2014df, author = {Cisneros, G Andr{\'e}s and Karttunen, Mikko and Ren, Pengyu and Sagui, Celeste}, title = {{Classical electrostatics for biomolecular simulations.}}, journal = {Chem. Rev}, year = {2014}, volume = {114}, number = {1}, pages = {779--814}, month = jan } @article{Capon:1961uw, author = {Capon, Jack}, title = {{A Note on the Asymptotic Normality of the Mann-Whitney-Wilcoxon Statistic}}, journal = {Journal of the American Statistical Association}, year = {1961}, volume = {56}, number = {295}, pages = {687--691}, month = sep } @article{Droege:2008kv, author = {Droege, Marcus and Hill, Brendon}, title = {{The genome sequencer FLX (TM) system-longer reads, more applications, straight forward bioinformatics and more complete data sets}}, journal = {J Biotechnol}, year = {2008}, volume = {136}, number = {1-2}, pages = {3--10} } @article{Hensen:2014jw, author = {Hensen, Ulf and Gr{\"a}ter, Frauke and Henchman, Richard H}, title = {{Macromolecular Entropy Can Be Accurately Computed from Force}}, journal = {J Chem Theory Comput}, year = {2014}, volume = {10}, number = {11}, pages = {4777--4781}, month = nov } @article{STEIGER:1980tz, author = {STEIGER, JH}, title = {{Tests for Comparing Elements of a Correlation Matrix}}, journal = {Psychol Bull}, year = {1980}, volume = {87}, number = {2}, pages = {245--251} } @article{Echave:2010tn, author = {Echave, Julian}, title = {{The meaning of the 1st term of bhat}}, year = {2010}, pages = {1--2}, month = jun } @article{Mintseris:2003va, author = {Mintseris, J and Weng, Z}, title = {{Atomic contact vectors in protein-protein recognition}}, journal = {Structure}, year = {2003} } @article{Berezovsky:2005ie, author = {Berezovsky, IN and Shakhnovich, EI}, title = {{Physics and evolution of thermophilic adaptation}}, journal = {Proc. Natl. Acad. Sci. U. S. A.}, year = {2005}, volume = {102}, number = {36}, pages = {12742--12747} } @article{Lomize:2011hl, author = {Lomize, Andrei L and Pogozheva, Irina D and Mosberg, Henry I}, title = {{Anisotropic solvent model of the lipid bilayer. 1. Parameterization of long-range electrostatics and first solvation shell effects.}}, journal = {J Chem Inf Model}, year = {2011}, volume = {51}, number = {4}, pages = {918--929}, month = apr } @article{Kobayashi:1967tf, author = {Kobayashi, H and Thomas, J B}, title = {{Distance measures and related criteria}}, journal = {Proc 5th Annu Allerton Conf \ldots}, year = {1967} } @article{Kamerlin:2013dz, author = {Kamerlin, Shina C L and Sharma, Pankaz K and Prasad, Ram B and Warshel, Arieh}, title = {{Why nature really chose phosphate}}, journal = {Quart. Rev. Biophys.}, year = {2013}, volume = {46}, number = {01}, pages = {1--132}, month = jan } @article{Monserud:2016gd, author = {Monserud, Jon H and Schwartz, Daniel K}, title = {{Interfacial Molecular Searching Using Forager Dynamics}}, journal = {Phys. Rev. Lett.}, year = {2016}, volume = {116}, number = {9}, pages = {098303}, month = mar } @article{BRUSCHWEILER:1995uw, author = {BRUSCHWEILER, R}, title = {{Collective Protein Dynamics and Nuclear-Spin Relaxation}}, journal = {J. Chem. Phys.}, year = {1995}, volume = {102}, number = {8}, pages = {3396--3403} } @article{McKee:2015fc, author = {McKee, Maggie}, title = {{Core Concept: Quantum turbulence:}}, journal = {Proc. Natl. Acad. Sci. U. S. A.}, year = {2015}, volume = {112}, number = {1}, pages = {4--5}, month = jan } @article{Lockless:1999uf, author = {Lockless, SW and Ranganathan, R}, title = {{Evolutionarily conserved pathways of energetic connectivity in protein families}}, journal = {Science}, year = {1999}, volume = {286}, number = {5438}, pages = {295--299} } @webpage{Anonymous:gE69wMX8, title = {{The spreading of misinformation online}}, url = {http://www.pnas.org/content/113/3/554.abstract.html?etoc} } @article{Dessailly:2010tv, author = {Dessailly, B and Redfern, O and Cuff, A}, title = {{Detailed Analysis of Function Divergence in a Large and Diverse Domain Superfamily: Toward a Refined Protocol of Function Classification}}, journal = {Structure}, year = {2010} } @article{Porter:2004ui, author = {Porter, Craig T and Bartlett, Gail J and Thornton, Janet M}, title = {{The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data}}, journal = {Nucleic Acids Res.}, year = {2004} } @article{Davis:2014do, author = {Davis, Meir and Tobi, Dror}, title = {{Multiple Gaussian Network Modes alignment reveals dynamically variable regions: The hemoglobin case}}, journal = {Proteins: Struct., Funct., Bioinf.}, year = {2014}, pages = {n/a--n/a}, month = mar } @article{Almeida:2014dl, author = {Almeida, Paulo F}, title = {{The Many Faces of Lipid Rafts}}, journal = {Biophys. J.}, year = {2014}, volume = {106}, number = {9}, pages = {1841--1843}, month = may } @techreport{Anonymous:0m8PCmhe, title = {{ICES WKPICS3 REPORT 2013}}, year = {2016}, month = nov } @article{Bousquet:2009wn, author = {Bousquet, Olivier and Boucheron, St{\'e}phane and Lugosi, G{\'a}bot}, title = {{Introduction to Statistical Learning Theory}}, year = {2009}, pages = {1--39}, month = feb } @article{Na:2014dz, author = {Na, Hyuntae and Song, Guang}, title = {{Conventional NMA as a better standard for evaluating elastic network models}}, journal = {Proteins: Struct., Funct., Bioinf.}, year = {2014}, pages = {n/a--n/a}, month = dec } @article{Redfern:2007uw, author = {Redfern, O and Harrison, A and Dallman, T and Pearl, F}, title = {{CATHEDRAL: A fast and effective algorithm to predict folds and domain boundaries from}}, journal = {bioinformatics.essex.ac.uk}, year = {2007} } @article{Borenstein:2009bx, author = {Borenstein, Elhanan and Feldman, Marcus W}, title = {{Topological Signatures of Species Interactions in Metabolic Networks}}, journal = {J Comput Biol}, year = {2009}, volume = {16}, number = {2}, pages = {191--200}, month = feb } @article{Hinsen:1999vb, author = {Hinsen, Konrad and Thomas, Aline and Field, MJ}, title = {{Analysis of domain motions in large proteins}}, journal = {Proteins: Struct., Funct., Bioinf.}, year = {1999}, volume = {34}, number = {3}, pages = {369--382} } @article{Romanowska:2012ck, author = {Romanowska, Julia and Nowi{\'{n}}ski, Krzysztof S and Trylska, Joanna}, title = {{Determining Geometrically Stable Domains in Molecular Conformation Sets}}, journal = {J Chem Theory Comput}, year = {2012}, volume = {8}, number = {8}, pages = {2588--2599}, month = aug } @article{Woodson:2010br, author = {Woodson, Sarah A}, title = {{Compact Intermediates in RNA Folding}}, journal = {Annu. Rev. Biophys.}, year = {2010}, volume = {39}, number = {1}, pages = {61--77}, month = apr } @article{Ambroso:vq, author = {Ambroso, Mark R and Hegde, Balachandra G and Langen, Ralf}, title = {{Endophilin A1 induces different membrane shapes using a conformational switch that is regulated by phosphorylation}}, journal = {pnas.org} } @article{Anonymous:ekDx6G-D, title = {{Stephen Wolfram: A New Kind of Science | Online{\textemdash}Table of Contents}} } @article{Berg:2006dy, author = {Berg, J}, title = {{Cross-species analysis of biological networks by Bayesian alignment}}, journal = {Proc. Natl. Acad. Sci. U. S. A.}, year = {2006}, volume = {103}, number = {29}, pages = {10967--10972}, month = jul } @webpage{Anonymous:8oQ-eRcj, title = {{PLoS ONE: Probing Molecular Mechanisms of the Hsp90 Chaperone: Biophysical Modeling Identifies Key Regulators of Functional Dynamics}}, url = {http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0037605} } @webpage{Anonymous:ARLpJqi2, title = {{Phys. Rev. Lett. 114, 118301 (2015) - Electrohydrodynamics Near Hydrophobic Surfaces}}, url = {http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.114.118301} } @article{Damm:2006ve, author = {Damm, KL and Carlson, HA}, title = {{Gaussian-weighted RMSD superposition of proteins: a structural comparison for flexible proteins and predicted protein structures}}, journal = {Biophys. J.}, year = {2006}, volume = {90}, number = {12}, pages = {4558--4573} } @article{Zachowski:1993un, author = {Zachowski, A}, title = {{Phospholipids in animal eukaryotic membranes: transverse asymmetry and movement.}}, journal = {Biochem J}, year = {1993}, volume = {294}, number = {Pt 1}, pages = {1}, month = aug } @article{Hinsen:2011bq, author = {Hinsen, Konrad}, title = {{A data and code model for reproducible research and executable papers}}, journal = {Procedia Computer Science}, year = {2011}, volume = {4}, pages = {579--588}, month = jan } @article{Fang:2014ix, author = {Fang, Jing and Nevin, Philip and Kairys, Visvaldas and Venclovas, {\v C}eslovas and Engen, John R and Beuning, Penny J}, title = {{Conformational Analysis of Processivity Clamps in Solution Demonstrates that Tertiary Structure Does Not Correlate with Protein Dynamics}}, journal = {Structure}, year = {2014}, volume = {22}, number = {4}, pages = {572--581}, month = apr } @article{HOPKINS:1991te, author = {HOPKINS, C C E and NILSSEN, E M}, title = {{The rise and fall of the Barents Sea capelin (Mallotus villosus): a multivariate scenario}}, journal = {Polar Research}, year = {1991}, volume = {10}, number = {2}, pages = {535--546}, month = dec } @article{Gjosaeter:2002hp, author = {Gjosaeter, H and Bogstad, B and Tjelmeland, S}, title = {{Assessment methodology for Barents Sea capelin, Mallotus villosus (Muller)}}, journal = {ICES J. Mar. Sci.}, year = {2002}, volume = {59}, number = {5}, pages = {1086--1095}, month = oct } @article{Zacharias:2002wq, author = {Zacharias, Niki and Dougherty, Dennis A}, title = {{Cation{\textendash}$\pi$ interactions in ligand recognition and catalysis}}, journal = {Trends in pharmacological sciences}, year = {2002}, volume = {23}, number = {6}, pages = {281--287} } @article{Neale:2014et, author = {Neale, Chris and Hsu, Jenny C Y and Yip, Christopher M and Pom{\`e}s, R{\'e}gis}, title = {{Indolicidin Binding Induces Thinning of a Lipid Bilayer}}, journal = {Biophys. J.}, year = {2014}, volume = {106}, number = {8}, pages = {L29--L31}, month = apr } @article{Shaw:2009vg, author = {Shaw, DE and Dror, RO and Salmon, JK and Grossman, JP and Mackenzie, KM and Bank, JA and Young, C and Deneroff, MM and Batson, B and Bowers, KJ}, title = {{Millisecond-scale molecular dynamics simulations on Anton}}, journal = {Proceedings of the Conference on High Performance Computing Networking, Storage and Analysis}, year = {2009}, pages = {1--11} } @article{Chouard:2011eq, author = {Chouard, Tanguy}, title = {{Breaking the protein rules}}, journal = {Nature}, year = {2011}, volume = {471}, number = {7337}, pages = {151--153} } @article{Maggi:2014dt, author = {Maggi, Claudio and Paoluzzi, Matteo and Pellicciotta, Nicola and Lepore, Alessia and Angelani, Luca and Di Leonardo, Roberto}, title = {{Generalized Energy Equipartition in Harmonic Oscillators Driven by Active Baths}}, journal = {Phys. Rev. Lett.}, year = {2014}, volume = {113}, number = {23}, pages = {238303}, month = dec } @article{Keskin:2007km, author = {Keskin, Ozlem}, title = {{Binding induced conformational changes of proteins correlate with their intrinsic fluctuations: a case study of antibodies}}, journal = {BMC Structural Biology}, year = {2007}, volume = {7}, number = {1}, pages = {31}, month = may } @article{Rodgers:2013hta, author = {Rodgers, Thomas L and Townsend, Philip D and Burnell, David and Jones, Matthew L and Richards, Shane A and McLeish, Tom C B and Pohl, Ehmke and Wilson, Mark R and Cann, Martin J}, title = {{Modulation of Global Low-Frequency Motions Underlies Allosteric Regulation: Demonstration in CRP/FNR Family Transcription Factors}}, journal = {PLoS Biol}, year = {2013}, volume = {11}, number = {9}, pages = {e1001651}, month = sep } @article{Lazebnik:xyT5MEf9, author = {Lazebnik, Yuri}, title = {{Can a biologist fix a radio?{\textemdash}Or, what I learned while studying apoptosis}}, year = {2002}, pages = {4}, month = aug } @article{Marianayagam:2005vm, author = {Marianayagam, N and Jackson, S}, title = {{Native-state dynamics of the ubiquitin family: implications for function and evolution}}, journal = {Journal of The Royal Society Interface}, year = {2005} } @article{Dalziel:2010hn, author = {Dalziel, Benjamin D and Morales, Juan M and Fryxell, John M}, title = {{Fitting Dynamic Models to Animal Movement Data: The Importance of Probes for Model Selection, a Reply to Franz and Caillaud}}, journal = {Am Nat}, year = {2010}, volume = {175}, number = {6}, pages = {762--764}, month = jun } @article{Fawcett:wy, author = {Fawcett, Tom}, title = {{ROC Graphs: Notes and Practical Considerations for Data Mining Researchers}} } @article{Lehmann:1951un, author = {Lehmann, E L}, title = {{Consistency and Unbiasedness of Certain Nonparametric Tests}}, journal = {The Annals of Mathematical Statistics}, year = {1951}, volume = {22}, number = {2}, pages = {165--179}, month = jun } @article{Cooper:2010vt, author = {Cooper, Seth and Treuille, Adrien and Barbero, Janos and Leaver-Fay, Andrew and Tuite, Kathleen and Khatib, Firas and Snyder, Alex Cho and Beenen, Michael and Salesin, David and Baker, David and Popovic, Zoran}, title = {{The challenge of designing scientific discovery games}}, year = {2010}, pages = {1--8}, month = may } @article{Norbury:2000wl, author = {Norbury, John W}, title = {{Lagrangians and Hamiltonians for High School Students}}, journal = {arXiv}, year = {2000}, eprint = {physics/0004029v1}, eprinttype = {arxiv}, eprintclass = {physics.ed-ph}, month = apr, annote = {Latex, 5 pages, 0 figures} } @article{Johnson:1999wc, author = {Johnson, J E and Cornell, R B}, title = {{Amphitropic proteins: regulation by reversible membrane interactions (review)}}, journal = {Mol Membr Biol}, year = {1999} } @article{Hurley:2002tr, author = {Hurley, James H and Misra, Saurav}, title = {{Signaling and Subcellular Targeting by Membrane-Binding Domains}}, year = {2002}, month = nov } @article{Nilges:2008kp, author = {Nilges, Michael and Bernard, Aymeric and Bardiaux, Benjamin and Malliavin, Th{\'e}r{\`e}se and Habeck, Michael and Rieping, Wolfgang}, title = {{Accurate NMR Structures Through Minimization of an Extended Hybrid Energy}}, journal = {Structure}, year = {2008}, volume = {16}, number = {9}, pages = {1305--1312}, month = sep } @webpage{Anonymous:IDmKKjJD, title = {{maxent_23_3622%5b0%5d.pdf}}, url = {http://www.kyb.tue.mpg.de/fileadmin/user_upload/files/publications/attachments/maxent_23_3622%5b0%5d.pdf} } @article{Marsh:2011ds, author = {Marsh, Joseph A and Teichmann, Sarah A}, title = {{Relative Solvent Accessible Surface Area Predicts Protein Conformational Changes upon Binding}}, journal = {Structure}, year = {2011}, volume = {19}, number = {6}, pages = {859--867}, month = jun } @article{Forman:2002wc, author = {Forman}, title = {{A Method for Discovering the Insignificance of One's Best Classifier and the Unlearnability of a Classification Task}}, year = {2002}, pages = {1--6}, month = may } @article{Krebs:2002fr, author = {Krebs, W G and Alexandrov, Vadim and Wilson, Cyrus A and Echols, Nathaniel and Yu, Haiyuan and Gerstein, Mark}, title = {{Normal mode analysis of macromolecular motions in a database framework: Developing mode concentration as a useful classifying statistic}}, journal = {Proteins: Struct., Funct., Bioinf.}, year = {2002}, volume = {48}, number = {4}, pages = {682--695}, month = aug } @article{Schotte:2004bk, author = {Schotte, Friedrich F and Soman, Jayashree J and Olson, John S JS and Wulff, Michael M and Anfinrud, Philip A PA}, title = {{Picosecond time-resolved X-ray crystallography: probing protein function in real time}}, journal = {Journal of structural biology}, year = {2004}, volume = {147}, number = {3}, pages = {235--246} } @article{Ma:2005gy, author = {Ma, J}, title = {{Usefulness and Limitations of Normal Mode Analysis in Modeling Dynamics of Biomolecular Complexes}}, journal = {Structure}, year = {2005}, volume = {13}, number = {3}, pages = {373--380}, month = mar } @article{Sanderson:2004by, author = {Sanderson, John M and Whelan, Eleanor J}, title = {{Characterisation of the interactions of aromatic amino acids with diacetyl phosphatidylcholinePresented at the Biophysical Chemistry Conference 2003, Warwick, UK, July 21?23, 2003.}}, journal = {Phys. Chem. Chem. Phys.}, year = {2004}, volume = {6}, number = {5}, pages = {1012} } @article{Tanford:TQr4ZqhF, author = {Tanford, Charles}, title = {{Interfacial free energy and the hydrophobic effect}}, journal = {pnas.org} } @article{Rufener:2005ie, author = {Rufener, Elisabeth and Frazier, April A and Wieser, Catherine M and Hinderliter, Anne and Cafiso, David S}, title = {{Membrane-Bound Orientation and Position of the Synaptotagmin C2B Domain Determined by Site-Directed Spin Labeling {\dag}}}, journal = {Biochemistry}, year = {2005}, volume = {44}, number = {1}, pages = {18--28}, month = jan } @article{Eidhammer:2000txa, author = {Eidhammer, I and Jonassen, I and Taylor, WR}, title = {{Structure comparison and structure patterns}}, journal = {J Comput Biol}, year = {2000}, volume = {7}, number = {5}, pages = {685--716} } @article{TANNER:1993uy, author = {TANNER, JJ and SMITH, PE and KRAUSE, KL}, title = {{Molecular-Dynamics Simulations and Rigid-Body (Tls) Analysis of Aspartate Carbamoyltransferase - Evidence for an Uncoupled R-State}}, journal = {Protein Sci.}, year = {1993}, volume = {2}, number = {6}, pages = {927--935} } @article{Jorgensen:1983fl, author = {Jorgensen, William L and Chandrasekhar, Jayaraman and Madura, Jeffry D and Impey, Roger W and Klein, Michael L}, title = {{Comparison of simple potential functions for simulating liquid water}}, journal = {J. Chem. Phys.}, year = {1983}, volume = {79}, number = {2}, pages = {926--935} } @article{Cooper:vd, author = {Cooper, S and Khatib, F and Treuille, A and Barbero, J and Lee, J}, title = {{Predicting protein structures with a multiplayer online game}}, journal = {Nature}, year = {2010}, month = aug } @inproceedings{Jana:2003fa, author = {Jana, S and Moulin, P}, title = {{IEEE Workshop on Statistical Signal Processing, 2003}}, booktitle = {IEEE Workshop on Statistical Signal Processing, 2003}, year = {2003}, pages = {625--628}, publisher = {IEEE} } @article{Capaldi:1972ul, author = {Capaldi, R A and Vanderkooi, G}, title = {{The low polarity of many membrane proteins.}}, journal = {Proc Natl Acad Sci U S A}, year = {1972}, volume = {69}, number = {4}, pages = {930--932}, month = apr } @article{NogalesCadenas:ty, author = {Nogales-Cadenas, R and Jonic, S and Tama, F and Arteni, A A and Tabas-Madrid, D and V{\'a}zquez, M and Pascual-Montano, A and Sorzano, C O S}, title = {{3DEM Loupe: analysis of macromolecular dynamics using structures from electron microscopy}} } @article{Malmberg:2003uk, author = {Malmberg, N J and Van Buskirk, D R and Falke, J J}, title = {{Membrane-Docking Loops of the cPLA2 C2 Domain:  Detailed Structural Analysis of the Protein{\textminus}Membrane Interface via Site-Directed Spin-Labeling - Biochemistry (ACS Publications)}}, journal = {Biochemistry}, year = {2003} } @article{Deng:vk, author = {Deng, Lizong and Wu, Aiping and Dai, Wentao and Song, Tingrui and Cui, Ya and Jiang, Taijiao}, title = {{Exploring protein domain organization by recognition of secondary structure packing interfaces}}, journal = {bioinformatics.oxfordjournals.org} } @article{Damasco:2017hw, author = {Damasco, Achille and Giuliani, Alessandro}, title = {{A resonance based model of biological evolution}}, journal = {Physica A: Statistical Mechanics and its Applications}, year = {2017}, volume = {471}, pages = {750--756}, month = apr } @article{LeoMacias:2005bd, author = {Leo-Macias, A and Lopez-Romero, P and Lupyan, D and Zerbino, D and Ortiz, AR}, title = {{An analysis of core deformations in protein superfamilies}}, journal = {Biophys. J.}, year = {2005}, volume = {88}, number = {2}, pages = {1291--1299} } @article{Dean:2007iy, author = {Dean, Antony M and Thornton, Joseph W}, title = {{Mechanistic approaches to the study of evolution: the functional synthesis}}, journal = {Nat Rev Genet}, year = {2007}, volume = {8}, number = {9}, pages = {675}, month = sep } @article{HenzlerWildman:2007cz, author = {Henzler-Wildman, Katherine A and Lei, Ming and Thai, Vu and Kerns, S Jordan and Karplus, Martin and Kern, Dorothee}, title = {{A hierarchy of timescales in protein dynamics is linked to enzyme catalysis}}, journal = {Nature}, year = {2007}, volume = {450}, number = {7171}, pages = {913--U27} } @article{Gerber:2002fp, author = {Gerber, S H and Rizo, J and Sudhof, T C}, title = {{Role of Electrostatic and Hydrophobic Interactions in Ca2+-Dependent Phospholipid Binding by the C2A-Domain From Synaptotagmin I}}, journal = {Diabetes}, year = {2002}, volume = {51}, number = {Supplement 1}, pages = {S12--S18}, month = feb } @article{Giugliarelli:2000ue, author = {Giugliarelli, G and Micheletti, C and Banavar, JR and Maritan, A}, title = {{Compactness, aggregation, and prionlike behavior of protein: A lattice model study}}, journal = {J. Chem. Phys.}, year = {2000}, volume = {113}, number = {12}, pages = {5072--5077} } @article{Micheletti:2004kn, author = {Micheletti, C and Carloni, P and Maritan, A}, title = {{Accurate and efficient description of protein vibrational dynamics: Comparing molecular dynamics and Gaussian models}}, journal = {Proteins: Struct., Funct., Bioinf.}, year = {2004}, volume = {55}, number = {3}, pages = {635--645} } @article{Gallego:2010ez, author = {Gallego, Oriol and Betts, Matthew J and Gvozdenovic-Jeremic, Jelena and Maeda, Kenji and Matetzki, Christian and Aguilar-Gurrieri, Carmen and Beltran-Alvarez, Pedro and Bonn, Stefan and Fern{\'a}ndez-Tornero, Carlos and Jensen, Lars Juhl and Kuhn, Michael and Trott, Jamie and Rybin, Vladimir and M{\"u}ller, Christoph W and Bork, Peer and Kaksonen, Marko and Russell, Robert B and Gavin, Anne-Claude}, title = {{A systematic screen for protein{\textendash}lipid interactions in Saccharomyces cerevisiae}}, journal = {Mol Syst Biol}, year = {2010}, volume = {6}, month = nov } @article{Harley:2001ig, author = {Harley, Shelton J and Myers, Ransom A and Dunn, Alistair}, title = {{Is catch-per-unit-effort proportional to abundance?}}, journal = {Canadian Journal of Fisheries and Aquatic Sciences}, year = {2001}, volume = {58}, number = {9}, pages = {1760--1772} } @article{Jeschke:2012bi, author = {Jeschke, Gunnar}, title = {{A comparative study of structures and structural transitions of secondary transporters with the LeuT fold}}, journal = {Eur Biophys J}, year = {2012}, volume = {42}, number = {2-3}, pages = {181--197}, month = may } @article{Elber:1986bm, author = {Elber, R and Karplus, M}, title = {{Low-Frequency Modes in Proteins: Use of the Effective-Medium Approximation $_{to }$Interpret the Fractal Dimension Observed in Electron-Spin Relaxation Measurements}}, journal = {Phys. Rev. Lett.}, year = {1986}, volume = {56}, number = {4}, pages = {394--397}, month = jan } @article{Patrascioiu:1987tc, author = {Patrascioiu, A}, title = {{The Ergodic Hypothesis: A Complicated Problem in Mathematics and Physics}}, journal = {Los Alamos Science, Special Issue}, year = {1987}, pages = {263--279} } @article{Wolfenden:2015ib, author = {Wolfenden, Richard and Lewis, Charles A and Yuan, Yang and Carter, Charles W}, title = {{Temperature dependence of amino acid hydrophobicities.}}, journal = {Proc. Natl. Acad. Sci. U. S. A.}, year = {2015}, month = jun } @article{Capitani:2016fk, author = {Capitani, Guido and Duarte, Jose M and Baskaran, Kumaran and Bliven, Spencer and Somody, Joseph C}, title = {{Understanding the fabric of protein crystals: computational classification of biological interfaces and crystal contacts}}, journal = {Bioinformatics}, year = {2016}, volume = {32}, number = {4}, pages = {481--489}, month = feb } @article{Rozmanov:2014fe, author = {Rozmanov, Dmitri and Baoukina, Svetlana and Tieleman, D Peter}, title = {{Density based visualization for molecular simulation}}, journal = {Faraday Discuss.}, year = {2014}, volume = {169}, number = {0}, pages = {225--243}, month = jun } @article{Ramanathan:2011jo, author = {Ramanathan, Arvind A and Agarwal, Pratul K PK}, title = {{Evolutionarily conserved linkage between enzyme fold, flexibility, and catalysis.}}, journal = {PLoS Biol}, year = {2011}, volume = {9}, number = {11}, pages = {e1001193--e1001193}, month = oct } @article{Moore:2015fy, author = {Moore, Calvin C}, title = {{Ergodic theorem, ergodic theory, and statistical mechanics}}, journal = {Proc. Natl. Acad. Sci. U. S. A.}, year = {2015}, pages = {1907--1911}, month = feb } @article{VanWynsberghe:2010dx, author = {Van Wynsberghe, Adam W and Cui, Qiang}, title = {{Conservation and Variation of Structural Flexibility in Protein Families}}, journal = {Structure}, year = {2010}, volume = {18}, number = {3}, pages = {281--283}, month = mar } @webpage{Braverman:vj, author = {Braverman, M and J, Schneider}, title = {{Space-Bounded Church-Turing Thesis and Computational Tractability of Closed Systems }}, url = {http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.115.098701} } @article{Xu:2003gr, author = {Xu, C Y and Tobi, D and Bahar, I}, title = {{Allosteric changes in protein structure computed by a simple mechanical model: Hemoglobin T R2 transition}}, journal = {J. Mol. Biol.}, year = {2003}, volume = {333}, number = {1}, pages = {153--168} } @article{Shaw:2007uq, author = {Shaw, DE and Deneroff, MM and Dror, RO and Kuskin, JS and Larson, RH and Salmon, JK and Young, C and Batson, B and Bowers, KJ and Chao, JC}, title = {{Anton, a special-purpose machine for molecular dynamics simulation}}, journal = {ACM SIGARCH Computer Architecture News}, year = {2007}, volume = {35}, number = {2}, pages = {12} } @article{Sadowski:2010we, author = {Sadowski, M}, title = {{On the evolutionary origins of" Fold Space Continuity": A study of topological convergence and divergence in mixed alpha-beta domains.}}, journal = {Journal of structural biology}, year = {2010} } @article{Weiss:2005hi, author = {Weiss, Kenneth M}, title = {{The phenogenetic logic of life}}, journal = {Nat Rev Genet}, year = {2005}, volume = {6}, number = {1}, pages = {36--45} } @article{Pullum:2000up, author = {Pullum, Geoffrey}, title = {{Scooping the Loop Snooper}}, journal = {Mathematics Magazine}, year = {2000}, volume = {73}, number = {4}, pages = {319--320}, month = oct } @webpage{Anonymous:DZ0Twhd6, title = {{Phys. Rev. Lett. 113, 148103 (2014) - Thermodynamics of Statistical Inference by Cells}}, url = {http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.113.148103} } @article{McIntosh:paJnX6fO, author = {McIntosh, Thomas J and Simon, Sidney A}, title = {{Bilayers as Protein Solvents: Role of Bilayer Structure and Elastic Properties}}, journal = {jgp.rupress.org} } @webpage{Anonymous:hLm8vJgn, title = {{Complementary biophysical tools to investigate lipid specificity in the interaction between bioactive molecules and the plasma membrane: A review}}, url = {http://www.sciencedirect.com/science/article/pii/S0005273614003058} } @article{Anonymous:76f89qLl, title = {{For Review Only}}, year = {2017}, pages = {1--38}, month = feb } @manual{Anonymous:2015un, title = {{2016 Nissan LEAF | Owner's Manual | Nissan USA }}, month = aug, year = {2015} } @article{Gabdoulline:2001ht, author = {Gabdoulline, RR and Wade, RC}, title = {{Protein-protein association: Investigation of factors influencing association rates by Brownian dynamics simulations}}, journal = {J. Mol. Biol.}, year = {2001}, volume = {306}, number = {5}, pages = {1139--1155} } @article{Venditti:2009en, author = {Venditti, Chris and Meade, Andrew and Pagel, Mark}, title = {{Phylogenies reveal new interpretation of speciation and the Red Queen}}, journal = {Nature}, year = {2009}, month = dec } @webpage{Anonymous:2w74dQdC, title = {{PLOS Computational Biology: Combining Experiments and Simulations Using the Maximum Entropy Principle}}, url = {http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003406} } @article{Gabba:2014el, author = {Gabba, Matteo and Poblete, Sim{\'o}n and Rosenkranz, Tobias and Katranidis, Alexandros and Kempe, Daryan and Z{\"u}chner, Tina and Winkler, Roland G and Gompper, Gerhard and Fitter, J{\"o}rg}, title = {{Conformational State Distributions and Catalytically Relevant Dynamics of~a Hinge-Bending Enzyme Studied by Single-Molecule FRET and a Coarse-Grained Simulation}}, journal = {Biophys. J.}, year = {2014}, volume = {107}, number = {8}, pages = {1913--1923}, month = oct } @article{Lomize:2006jn, author = {Lomize, Andrei L and Pogozheva, Irina D and Lomize, Mikhail A and Mosberg, Henry I}, title = {{Positioning of proteins in membranes: a computational approach.}}, journal = {Protein Sci.}, year = {2006}, volume = {15}, number = {6}, pages = {1318--1333}, month = jun } @article{Marek:2015dw, author = {Marek, Antonin and Tang, Wenxing and Milikisiyants, Sergey and Nevzorov, Alexander A and Smirnov, Alex I}, title = {{Nanotube Array Method for Studying Lipid-Induced Conformational Changes of a Membrane Protein by Solid-State NMR}}, journal = {Biophys. J.}, year = {2015}, volume = {108}, number = {1}, pages = {5--9}, month = jan } @article{Zhou:1996cc, author = {Zhou, Huan-Xiang}, title = {{Effect of interaction potentials in diffusion-influenced reactions with small reactive regions}}, journal = {J. Chem. Phys.}, year = {1996}, volume = {105}, number = {16}, pages = {7235} } @article{Barut:1951js, author = {Barut, A}, title = {{Erratum: The Cathode Field in Diodes under Partial Space-Charge Conditions with Initial Velocities}}, journal = {Phys Rev}, year = {1951}, volume = {82}, number = {4}, pages = {554--554}, month = may } @article{Sterckx:2014ia, author = {Sterckx, Yann G J and Volkov, Alexander N and Vranken, Wim F and Kragelj, Jaka and Jensen, Malene Ringkj{\o}bing and Buts, Lieven and Garcia-Pino, Abel and Jov{\'e}, Thomas and Van Melderen, Laurence and Blackledge, Martin and van Nuland, Nico A J and Loris, Remy}, title = {{Small-Angle X-Ray Scattering- and Nuclear Magnetic Resonance-Derived Conformational Ensemble of the Highly Flexible Antitoxin PaaA2}}, journal = {Structure}, year = {2014}, volume = {22}, number = {6}, pages = {854--865}, month = jun } @article{Andersen:I_u9Mmq-, author = {Andersen, Olaf Sparre}, title = {{Perspectives on Membrane Protein Insertion, Protein{\textendash}Bilayer Interactions, and Amino Acid Side Hydrophobicity}}, journal = {jgp.rupress.org} } @article{Ball:2008hv, author = {Ball, Philip}, title = {{Water as an active constituent in cell biology.}}, journal = {Chem. Rev}, year = {2008}, volume = {108}, number = {1}, pages = {74--108}, month = jan } @article{Anonymous:SnxG2oom, title = {{hungarian}}, year = {2004}, pages = {8} } @article{Ghrist:2010tq, author = {Ghrist, Robert}, title = {{Applied algebraic topology and sensor networks}}, year = {2010}, pages = {1--74}, month = nov } @article{Smaldino:2016th, author = {Smaldino, Paul E and McElreath, Richard}, title = {{The Natural Selection of Bad Science}}, year = {2016}, month = may } @article{Kobayashi:1967tf, author = {Kobayashi, H and Thomas, J B}, title = {{Distance measures and related criteria}}, journal = {Proc 5th Annu Allerton Conf {\ldots}}, year = {1967} } @article{Anonymous:xynuDwyO, title = {{Matching}}, year = {2003}, pages = {6} } @article{Anonymous:PX_6j1uJ, title = {{nihms214757.pdf}} } @article{Nagle:2000wp, author = {Nagle, John F and Tristram-Nagle, Stephanie}, title = {{Lipid bilayer structure}}, journal = {Current Opinion in Structural Biology}, year = {2000}, volume = {10}, number = {4}, pages = {474--480} } @webpage{Anonymous:yT5NGPu-, title = {{Scientific method: Statistical errors : Nature News {\&} Comment}}, url = {http://www.nature.com/news/scientific-method-statistical-errors-1.14700} } @article{Wu:2011ds, author = {Wu, Zhe and Cui, Qiang and Yethiraj, Arun}, title = {{Driving Force for the Association of Hydrophobic Peptides: The Importance of Electrostatic Interactions in Coarse-Grained Water Models}}, journal = {J. Phys. Chem. Lett.}, year = {2011}, volume = {2}, number = {14}, pages = {1794--1798}, month = jul } @article{Bezem:2010wp, author = {Bezem, Marc}, title = {{A prolog compendium, October 4, 2010}}, year = {2010}, pages = {1--23}, month = oct }