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\bibstyle{plos2015}
\citation{Kutateladze:2010jz,Vogler:2008ch,Cullen:2008kv,Inaba:2016cb,Itoh:2005cp}
\citation{Lemmon:2008kt,Cho:2005bq}
\citation{Cho:2005bq,Johnson:1999wc}
\citation{MulgrewNesbitt:2006dy}
\citation{Lazaridis:2003wu}
\citation{Lomize:2007gm}
\citation{Gilbert:2002ja,Gamsjaeger:2005jd}
\citation{Lomize:2007gm}
\citation{Ford:2002if}
\citation{Lomize:2007gm,BalaliMood:2009cv,Lazaridis:2003wu}
\citation{Yang:2015fd}
\@writefile{lof}{\contentsline {figure}{\numberline {1}{\ignorespaces The definitions of \emph  {protrusions} and \emph  {co-insertable protruding hydrophobes}. Panel A shows a cartoon representation of the C2 domain of human phospholipase A\textsubscript  {2} (PDB ID: 1RLW), and panel B shows the convex hull for the same protein. Panels\nobreakspace  {}C and\nobreakspace  {}D show the same for an example with an aliphatic helix in the ENTH-domain (PDB ID: 1H0A). All C\textsubscript  {\textalpha }- and C\textsubscript  {\textbeta }-atoms are shown as spheres. Hydrophobes are coloured orange. The convex hull for the C\textsubscript  {\textalpha }- and C\textsubscript  {\textbeta }-atomic coordinates is shown in blue. All spheres visible on the convex-hull representation are vertex residues. \emph  {Protrusions} are defined as vertex residues with low local protein density, and shown as large spheres. \emph  {Co-insertable protruding hydrophobes} are protruding hydrophobes that are adjacent vertices of the convex hull, they are shown connected by orange lines. Small black spheres are at vertex residues that have high local density, and do therefore not meet the criteria for protrusions.\relax }}{4}{figure.caption.5}}
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\newlabel{FigModelIllustration}{{1}{4}{The definitions of \emph {protrusions} and \emph {co-insertable protruding hydrophobes}. Panel A shows a cartoon representation of the C2 domain of human phospholipase A\textsubscript {2} (PDB ID: 1RLW), and panel B shows the convex hull for the same protein. Panels~C and~D show the same for an example with an aliphatic helix in the ENTH-domain (PDB ID: 1H0A). All \ca /- and \cb /-atoms are shown as spheres. Hydrophobes are coloured orange. The convex hull for the \ca /- and \cb /-atomic coordinates is shown in blue. All spheres visible on the convex-hull representation are vertex residues. \emph {Protrusions} are defined as vertex residues with low local protein density, and shown as large spheres. \emph {Co-insertable protruding hydrophobes} are protruding hydrophobes that are adjacent vertices of the convex hull, they are shown connected by orange lines. Small black spheres are at vertex residues that have high local density, and do therefore not meet the criteria for protrusions.\relax }{figure.caption.5}{}}
\citation{Miller:1987un}
\@writefile{lof}{\contentsline {figure}{\numberline {2}{\ignorespaces Hydrophobes are more common on protruding positions in peripheral proteins, than in the reference sets. The plots show frequencies of hydrophobes on surface amino acids, both on protrusions (A, and C) and among all solvent exposed amino acids (B and D). Compare peripheral proteins (blue) and the non-binding surfaces (red). The horizontal axes show the mean fraction (Eq\nobreakspace  {}\ref  {eq:mean_frac_family}) of protrusions or solvent exposed amino-acids that are hydrophobic. The vertical axis shows the fraction of protein families for each set. A-D shows the comparison between the data sets \emph  {Peripheral} and \emph  {Non-binding surfaces}, and E-H the comparison between the \emph  {Peripheral-P } and \emph  {Reference proteins}.\relax }}{5}{figure.caption.7}}
\newlabel{FigProtrusionDensityHistograms}{{2}{5}{Hydrophobes are more common on protruding positions in peripheral proteins, than in the reference sets. The plots show frequencies of hydrophobes on surface amino acids, both on protrusions (A, and C) and among all solvent exposed amino acids (B and D). Compare peripheral proteins (\periphcolor /) and the non-binding surfaces (\tmcolor /). The horizontal axes show the mean fraction (Eq~\ref {eq:mean_frac_family}) of protrusions or solvent exposed amino-acids that are hydrophobic. The vertical axis shows the fraction of protein families for each set. A-D shows the comparison between the data sets \emph {Peripheral} and \emph {Non-binding surfaces}, and E-H the comparison between the \emph {Peripheral-P } and \emph {Reference proteins}.\relax }{figure.caption.7}{}}
\@writefile{lof}{\contentsline {figure}{\numberline {3}{\ignorespaces On peripheral proteins (the set \emph  {Peripheral}), protrusions in low density regions are more often hydrophobes, compared to the \emph  {Non-binding surfaces}. The plot shows the logarithm of the odds-ratio (Eq\nobreakspace  {}\ref  {eq:odds_ratio}) comparing the frequency of hydrophobes on \emph  {vertex} residues in peripheral proteins and the reference set. Positive values reflect higher frequencies in the peripheral proteins. The horizontal axis shows the protein density $d$ around the protrusion, measured as the number of C\textsubscript  {\textalpha } and C\textsubscript  {\textbeta } atoms within $1 nm$. Vertex residues are all on the convex hull, but only the vertex residues with $d<22$ are protrusions. The leftmost bar with $d<7$ corresponds mostly to chain terminals. More precisely, the vertical axis shows $\R  {\left (A, B,\mathaccentV {hat}05E{F}_{\mathrm  {hydrophobe}|\mathrm  {vertex}\cap l<d\leq u }\right )}$ where $A$ denotes the set \emph  {Peripheral}, $B$ the \emph  {Non-binding surfaces}, $l$ and $u$ denote the lower and upper limits of the ranges given on the vertical axis, and $d$ is the local protein density defined in\nobreakspace  {}\emph  {Materials and methods}. Error bars are 95\% confidence intervals.\relax }}{6}{figure.caption.8}}
\newlabel{FigNeighboursVsOddsRatio}{{3}{6}{On peripheral proteins (the set \emph {Peripheral}), protrusions in low density regions are more often hydrophobes, compared to the \emph {Non-binding surfaces}. The plot shows the logarithm of the odds-ratio (Eq~\ref {eq:odds_ratio}) comparing the frequency of hydrophobes on \emph {vertex} residues in peripheral proteins and the reference set. Positive values reflect higher frequencies in the peripheral proteins. The horizontal axis shows the protein density $d$ around the protrusion, measured as the number of \ca / and \cb / atoms within $1 nm$. Vertex residues are all on the convex hull, but only the vertex residues with $d<22$ are protrusions. The leftmost bar with $d<7$ corresponds mostly to chain terminals. More precisely, the vertical axis shows $\OR {A, B,\hat {F}_{\mathrm {hydrophobe}|\mathrm {vertex}\cap l<d\leq u }}$ where $A$ denotes the set \emph {Peripheral}, $B$ the \emph {Non-binding surfaces}, $l$ and $u$ denote the lower and upper limits of the ranges given on the vertical axis, and $d$ is the local protein density defined in~\matmet /. Error bars are 95\% confidence intervals.\relax }{figure.caption.8}{}}
\@writefile{lof}{\contentsline {figure}{\numberline {4}{\ignorespaces The \emph  {protruding hydrophobes} tend to be \emph  {co-insertable} in the peripheral proteins. The tendency for protrusions to be co-insertable is quantified by the weighted frequency of co-insertion (Eq\nobreakspace  {}\ref  {eq:coins_freq}), and is compared between each data set and a null model using the odds ratio (Eq\nobreakspace  {}\ref  {eq:odds_ratio}). Positive values reflect higher frequencies of co-insertion than in the null model. More precisely, we show the comparisons $\R  {\left (set,null,\mathaccentV {hat}05E{F}^{\mathrm  {pair}}_{\mathrm  {one},\mathrm  {both}}\right )}$, where $set$ represents the set of peripheral proteins (blue) and the reference set (red), and $null$ represent their respective null models where hydrophobes have been relocated randomly among protrusions as described in\nobreakspace  {}\emph  {Materials and methods}. Error bars are 95\% confidence intervals. Panel A shows the comparison between the data sets \emph  {Peripheral} and \emph  {Non-binding surfaces}, and B the comparison between the \emph  {Peripheral-P } and \emph  {Reference proteins}.\relax }}{7}{figure.caption.9}}
\newlabel{FigHfConditionals}{{4}{7}{The \emph {protruding hydrophobes} tend to be \emph {co-insertable} in the peripheral proteins. The tendency for protrusions to be co-insertable is quantified by the weighted frequency of co-insertion (Eq~\ref {eq:coins_freq}), and is compared between each data set and a null model using the odds ratio (Eq~\ref {eq:odds_ratio}). Positive values reflect higher frequencies of co-insertion than in the null model. More precisely, we show the comparisons $\OR {set,null,\hat {F}^{\mathrm {pair}}_{\mathrm {one},\mathrm {both}}}$, where $set$ represents the set of peripheral proteins (\periphcolor /) and the reference set (\tmcolor /), and $null$ represent their respective null models where hydrophobes have been relocated randomly among protrusions as described in~\matmet /. Error bars are 95\% confidence intervals. Panel A shows the comparison between the data sets \emph {Peripheral} and \emph {Non-binding surfaces}, and B the comparison between the \emph {Peripheral-P } and \emph {Reference proteins}.\relax }{figure.caption.9}{}}
\citation{Perisic:1998tv}
\citation{Bravo:2001ua}
\citation{Scott:1990wf}
\citation{Zhang:1995vz}
\citation{Ford:2002if}
\citation{Misra:1999uo}
\citation{Agasoster:2003bja}
\@writefile{lof}{\contentsline {figure}{\numberline {5}{\ignorespaces \emph  {Co-insertable protruding hydrophobes} are common in peripheral proteins and rare in the reference sets. The plots show the occurrence of \emph  {co-insertable protruding hydrophobes} on protein surfaces. Panels\nobreakspace  {}A,\nobreakspace  {}B,\nobreakspace  {}D, and\nobreakspace  {}E show the weighted fraction (Eq\nobreakspace  {}\ref  {eq:weighted_existance_frec}) of proteins that have protruding hydrophobes, in the peripheral proteins (blue) and the reference sets (red). We have differentiated here between protrusions that have at least one co-insertable protruding hydrophobe (labeled ``Co-ins.''), and those that have not (labeled ``isolated''). The analysis is done separately for two groups of proteins according to the total number of protrusions on the protein surface ($[0,25\delimiter "526930B $ in panels\nobreakspace  {}A and\nobreakspace  {}D, $[25,50\delimiter "526930B $ in panels\nobreakspace  {}B and\nobreakspace  {}E). Panels\nobreakspace  {}C and\nobreakspace  {}F shows the frequency distribution of the total number of protruding residues (``\# protrusions'') for all proteins. The selections analysed in panels\nobreakspace  {}A,\nobreakspace  {}B,\nobreakspace  {}D, and\nobreakspace  {}E are found between the dashed lines in panels\nobreakspace  {}C andF. Error bars in panels\nobreakspace  {}A,\nobreakspace  {}B,\nobreakspace  {}D, and\nobreakspace  {}E are 95\% confidence intervals. Panels\nobreakspace  {}A-C shows the comparison between the sets \emph  {Peripheral} and \emph  {Non-binding surfaces}, panels\nobreakspace  {}D-F, the comparison between \emph  {Peripheral-P } and \emph  {Reference proteins}.\relax }}{8}{figure.caption.10}}
\newlabel{FigContainingProtrusions}{{5}{8}{\emph {Co-insertable protruding hydrophobes} are common in peripheral proteins and rare in the reference sets. The plots show the occurrence of \emph {co-insertable protruding hydrophobes} on protein surfaces. Panels~A,~B,~D, and~E show the weighted fraction (Eq~\ref {eq:weighted_existance_frec}) of proteins that have protruding hydrophobes, in the peripheral proteins (\periphcolor /) and the reference sets (\tmcolor /). We have differentiated here between protrusions that have at least one co-insertable protruding hydrophobe (labeled ``Co-ins.''), and those that have not (labeled ``isolated''). The analysis is done separately for two groups of proteins according to the total number of protrusions on the protein surface ($[0,25\rangle $ in panels~A and~D, $[25,50\rangle $ in panels~B and~E). Panels~C and~F shows the frequency distribution of the total number of protruding residues (``\# protrusions'') for all proteins. The selections analysed in panels~A,~B,~D, and~E are found between the dashed lines in panels~C andF. Error bars in panels~A,~B,~D, and~E are 95\% confidence intervals. Panels~A-C shows the comparison between the sets \emph {Peripheral} and \emph {Non-binding surfaces}, panels~D-F, the comparison between \emph {Peripheral-P } and \emph {Reference proteins}.\relax }{figure.caption.10}{}}
\citation{Lomize:2007gm}
\@writefile{lof}{\contentsline {figure}{\numberline {6}{\ignorespaces Protruding hydrophobes are found on the membrane binding sites of well known membrane binding domains. The figure shows the convex hull (in blue) of the C\textsubscript  {\textalpha } and C\textsubscript  {\textbeta }-atoms of selected peripheral membrane binding domains. The C\textsubscript  {\textbeta }-atoms of \emph  {the Likely Inserted Hydrophobe} are shown as orange spheres and C\textsubscript  {\textbeta }-atoms of experimentally identified membrane-binding residues as gray spheres. The Likely Inserted Hydrophobe is an amino acid that has been experimentally verified to be a membrane binding residue for A, B, D and F. For C and E the Likely Inserted Hydrophobe is located in the same area as the residues identified by experiments. \textbf  {A}: C2 domain of human phospholipase A2 (PDBID: 1RLW\nobreakspace  {}\cite  {Perisic:1998tv}); \textbf  {B}: PX domain of P40PHOX (PDBID: 1H6H\nobreakspace  {}\cite  {Bravo:2001ua}); \textbf  {C}: snake phospholipase A2 (PDBID: 1POA\nobreakspace  {}\cite  {Scott:1990wf}); \textbf  {D} : C1 domain of protein kinase C delta (PDBID: 1PTR\nobreakspace  {}\cite  {Zhang:1995vz}); \textbf  {E}: Epsin ENTH domain (PDBID: 1H0A\nobreakspace  {}\cite  {Ford:2002if}); \textbf  {F}: FYVE domain of yeast vacuolar protein sorting-associated protein 27 (PDBID: 1VFY\nobreakspace  {}\cite  {Misra:1999uo}).\relax }}{9}{figure.caption.12}}
\newlabel{FigDomainExamples}{{6}{9}{Protruding hydrophobes are found on the membrane binding sites of well known membrane binding domains. The figure shows the convex hull (in blue) of the \ca / and \cb /-atoms of selected peripheral membrane binding domains. The \cb /-atoms of \emph {the Likely Inserted Hydrophobe} are shown as orange spheres and \cb /-atoms of experimentally identified membrane-binding residues as gray spheres. The Likely Inserted Hydrophobe is an amino acid that has been experimentally verified to be a membrane binding residue for A, B, D and F. For C and E the Likely Inserted Hydrophobe is located in the same area as the residues identified by experiments. \textbf {A}: C2 domain of human phospholipase A2 (PDBID: 1RLW~\cite {Perisic:1998tv}); \textbf {B}: PX domain of P40PHOX (PDBID: 1H6H~\cite {Bravo:2001ua}); \textbf {C}: snake phospholipase A2 (PDBID: 1POA~\cite {Scott:1990wf}); \textbf {D} : C1 domain of protein kinase C delta (PDBID: 1PTR~\cite {Zhang:1995vz}); \textbf {E}: Epsin ENTH domain (PDBID: 1H0A~\cite {Ford:2002if}); \textbf {F}: FYVE domain of yeast vacuolar protein sorting-associated protein 27 (PDBID: 1VFY~\cite {Misra:1999uo}).\relax }{figure.caption.12}{}}
\citation{Lomize:2011hl}
\citation{Lomize:2011iz}
\@writefile{lof}{\contentsline {figure}{\numberline {7}{\ignorespaces Protruding hydrophobes predict experimentally verified binding sites. The figure shows comparisons of predicted binding residues (\emph  {the Likely Inserted Hydrophobe}) with experimentally verified binding sites for a manually curated dataset of 24 proteins (listed in Table S2). The vertical axis corresponds to values of the angle (Eq\nobreakspace  {}\ref  {eq:orientation}) comparing the two vectors connecting the center of the protein with either the predicted or known binding sites. Smaller angles imply better agreement between prediction and experiment. Asterisks ($*$) mark proteins where the Likely Inserted Hydrophobe is an amino acid experimentally identified to be interacting with the membrane. The grey boxplots show the distribution of angles when the known binding site residues are compared to all protruding amino acids on the protein. 1iaz is analysed in its soluble monomeric state, while it forms a transmembrane pore upon oligomerisation. The structure of the Bovine $\alpha $-lactalbumin (PDBID: 1F6S) has no identified protruding hydrophobes and is marked with a cross at 180\degree  .\relax }}{10}{figure.caption.13}}
\newlabel{FigCompExperiment}{{7}{10}{Protruding hydrophobes predict experimentally verified binding sites. The figure shows comparisons of predicted binding residues (\emph {the Likely Inserted Hydrophobe}) with experimentally verified binding sites for a manually curated dataset of 24 proteins (listed in Table S2). The vertical axis corresponds to values of the angle (Eq~\ref {eq:orientation}) comparing the two vectors connecting the center of the protein with either the predicted or known binding sites. Smaller angles imply better agreement between prediction and experiment. Asterisks ($*$) mark proteins where the Likely Inserted Hydrophobe is an amino acid experimentally identified to be interacting with the membrane. The grey boxplots show the distribution of angles when the known binding site residues are compared to all protruding amino acids on the protein. 1iaz is analysed in its soluble monomeric state, while it forms a transmembrane pore upon oligomerisation. The structure of the Bovine $\alpha $-lactalbumin (PDBID: 1F6S) has no identified protruding hydrophobes and is marked with a cross at 180\degree .\relax }{figure.caption.13}{}}
\citation{Petsko:2004wf}
\@writefile{lof}{\contentsline {figure}{\numberline {8}{\ignorespaces Comparing predictions based on protruding hydrophobes with the predicted IBS in the Orientation of Proteins in Membranes (OPM) database. The plots show the distributions of the median \emph  {insertion coordinate} from OPM for \emph  {the Likely Inserted Hydrophobe} in each family (measured at the C\textsubscript  {\textalpha }-atom). Values greater than or equal to zero correspond to atoms positioned in the hydrophobic core or at the boundary. Hence insertion coordinate values close to zero indicate agreement with OPM. Panel\nobreakspace  {}A (C) show data for the Likely Inserted Hydrophobes and panel\nobreakspace  {}B (D) for a null model of randomly selected \emph  {protruding} residues. Panel\nobreakspace  {}C and\nobreakspace  {}D show cumulative histograms (accumulated with decreasing insertion coordinates).\relax }}{11}{figure.caption.15}}
\newlabel{FigLargestFacetLocation}{{8}{11}{Comparing predictions based on protruding hydrophobes with the predicted IBS in the Orientation of Proteins in Membranes (OPM) database. The plots show the distributions of the median \emph {insertion coordinate} from OPM for \emph {the Likely Inserted Hydrophobe} in each family (measured at the \ca /-atom). Values greater than or equal to zero correspond to atoms positioned in the hydrophobic core or at the boundary. Hence insertion coordinate values close to zero indicate agreement with OPM. Panel~A (C) show data for the Likely Inserted Hydrophobes and panel~B (D) for a null model of randomly selected \emph {protruding} residues. Panel~C and~D show cumulative histograms (accumulated with decreasing insertion coordinates).\relax }{figure.caption.15}{}}
\citation{Wimley:1996vpa}
\citation{Wilmot:1988vb}
\@writefile{lof}{\contentsline {figure}{\numberline {9}{\ignorespaces In peripheral proteins, hydrophobic protrusions are more frequent on turns, bends and $\alpha $-helices, compared to the reference set. Panel A shows the weighted number (Eq\nobreakspace  {}\ref  {eq:weighted_count}) of \emph  {protruding hydrophobes} associated with the different types of secondary structure elements. We have differentiated between protrusions that have at least one co-insertable protruding hydrophobe (right, labeled ``Co-ins.''), and those that have not (left, labeled ``Isolated''). Panel B compares the weighted frequencies (Eq\nobreakspace  {}\ref  {eq:weighted_frec}) of hydrophobes on protruding secondary structures between the peripheral membrane proteins and the reference set, using the odds ratio (Eq\nobreakspace  {}\ref  {eq:odds_ratio}). Positive values reflect higher frequencies in the peripheral proteins. More precisely, panel A show the values $N_{\mathrm  {hydrophobe}|\mathrm  {protrusion}\cap sse }$, and panel B the comparisons $\R  {\left (A,B, \mathaccentV {hat}05E{F}_{\mathrm  {hydrophobe}|\mathrm  {protrusion}\cap sse }\right )}$ where $A$ denote the peripheral proteins, $B$ the reference set, and $sse$ specifies the secondary structures given in the color legend. Error bars in panel B are 95\% confidence intervals.\relax }}{12}{figure.caption.17}}
\newlabel{FigSSE}{{9}{12}{In peripheral proteins, hydrophobic protrusions are more frequent on turns, bends and $\alpha $-helices, compared to the reference set. Panel A shows the weighted number (Eq~\ref {eq:weighted_count}) of \emph {protruding hydrophobes} associated with the different types of secondary structure elements. We have differentiated between protrusions that have at least one co-insertable protruding hydrophobe (right, labeled ``Co-ins.''), and those that have not (left, labeled ``Isolated''). Panel B compares the weighted frequencies (Eq~\ref {eq:weighted_frec}) of hydrophobes on protruding secondary structures between the peripheral membrane proteins and the reference set, using the odds ratio (Eq~\ref {eq:odds_ratio}). Positive values reflect higher frequencies in the peripheral proteins. More precisely, panel A show the values $N_{\mathrm {hydrophobe}|\mathrm {protrusion}\cap sse }$, and panel B the comparisons $\OR {A,B, \hat {F}_{\mathrm {hydrophobe}|\mathrm {protrusion}\cap sse }}$ where $A$ denote the peripheral proteins, $B$ the reference set, and $sse$ specifies the secondary structures given in the color legend. Error bars in panel B are 95\% confidence intervals.\relax }{figure.caption.17}{}}
\@writefile{lof}{\contentsline {figure}{\numberline {10}{\ignorespaces Large aliphatic and aromatic side chains are particularly over-represented on protrusion on peripheral proteins. Panel A shows the weighted fractions (Eq\nobreakspace  {}\ref  {eq:weighted_frec}) of hydrophobic amino acids on protrusions from peripheral proteins (blue) and from proteins in the reference set (red). In panel B, the contrast between the two sets is quantified by the odds ratio (Eq\nobreakspace  {}\ref  {eq:odds_ratio}), so that positive values reflect higher frequencies in the set of peripheral proteins than in the reference set. More precisely the vertical axis denote $\qopname  \relax o{ln}\R  {\left (\mathrm  {peripheral}, \mathrm  {reference}, \mathaccentV {hat}05E{F}_{aa, \mathrm  {protrusion}}\right )}$, with $aa$ representing each of the standard amino acids. Error bars are 95\% confidence intervals.\relax }}{13}{figure.caption.18}}
\newlabel{FigTmPeriphAaComparison}{{10}{13}{Large aliphatic and aromatic side chains are particularly over-represented on protrusion on peripheral proteins. Panel A shows the weighted fractions (Eq~\ref {eq:weighted_frec}) of hydrophobic amino acids on protrusions from peripheral proteins (\periphcolor /) and from proteins in the reference set (\tmcolor /). In panel B, the contrast between the two sets is quantified by the odds ratio (Eq~\ref {eq:odds_ratio}), so that positive values reflect higher frequencies in the set of peripheral proteins than in the reference set. More precisely the vertical axis denote $\ln \OR {\mathrm {peripheral}, \mathrm {reference}, \hat {F}_{aa, \mathrm {protrusion}}}$, with $aa$ representing each of the standard amino acids. Error bars are 95\% confidence intervals.\relax }{figure.caption.18}{}}
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\@writefile{lof}{\contentsline {figure}{\numberline {11}{\ignorespaces Differences in number of polypeptide chains between the protein models present in the \emph  {Peripheral} (quaternary structure model from OPM) and the models in \emph  {Peripheral-P } (quaternary structure model predicted by PISA). The difference is calculated for each of the PDB IDs occurring in both datasets. When more chains are present in the PISA models, The difference (horisontal axis) is negative.\relax }}{17}{figure.caption.23}}
\newlabel{FigOligomerComparison}{{11}{17}{Differences in number of polypeptide chains between the protein models present in the \emph {Peripheral} (quaternary structure model from OPM) and the models in \emph {Peripheral-P } (quaternary structure model predicted by PISA). The difference is calculated for each of the PDB IDs occurring in both datasets. When more chains are present in the PISA models, The difference (horisontal axis) is negative.\relax }{figure.caption.23}{}}
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\newlabel{eq:weighted_frec}{{4}{19}{Averages of residues}{equation.0.4}{}}
\newlabel{eq:weighted_existance_frec}{{5}{19}{Averages of residues}{equation.0.5}{}}
\newlabel{eq:coins_existance_freq}{{8}{20}{Averages of co-insertable pairs}{equation.0.8}{}}
\newlabel{eq:coins_freq}{{9}{20}{Averages of co-insertable pairs}{equation.0.9}{}}
\newlabel{eq:odds_ratio}{{10}{20}{Comparison between data sets}{equation.0.10}{}}
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\newlabel{S2_Set}{{}{21}{S2 Data Set}{section*.39}{}}
\newlabel{S3_Set}{{}{21}{S3 Data Set}{section*.40}{}}
\newlabel{S4_Set}{{}{21}{S4 Data Set}{section*.41}{}}
\bibdata{library}
\bibcite{Kutateladze:2010jz}{1}
\bibcite{Vogler:2008ch}{2}
\bibcite{Cullen:2008kv}{3}
\bibcite{Inaba:2016cb}{4}
\bibcite{Itoh:2005cp}{5}
\bibcite{Lemmon:2008kt}{6}
\bibcite{Cho:2005bq}{7}
\bibcite{Johnson:1999wc}{8}
\bibcite{MulgrewNesbitt:2006dy}{9}
\bibcite{Lazaridis:2003wu}{10}
\bibcite{Lomize:2007gm}{11}
\newlabel{S5_Set}{{}{22}{S5 Data Set}{section*.42}{}}
\bibcite{Gilbert:2002ja}{12}
\bibcite{Gamsjaeger:2005jd}{13}
\bibcite{Ford:2002if}{14}
\bibcite{BalaliMood:2009cv}{15}
\bibcite{Yang:2015fd}{16}
\bibcite{Miller:1987un}{17}
\bibcite{Perisic:1998tv}{18}
\bibcite{Bravo:2001ua}{19}
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