Comparison of distributions of alignment identities and similarities between alignments containing all interface residues and all alignments.

<p>The distributions of alignments containing all interface residues are shown by open bars and those of all alignments are shown by closed bars. Panels A and C show distributions for the alignments with maximum query sequence coverage 40% and panels B and D show the distributions for the whole alignment pool irrespectively of query sequence coverage.</p

Probability of finding all interface residues inside an alignment as a function of alignment identity and similarity.

<p>Curves are least-square polynomial fits to the data points obtained from the analysis of PSI-BLAST alignments for the representative set of 329 complexes used in the study.</p

Percentage of alignments with full interface coverage (FIC alignments) in alignment pool produced by PSI-BLAST on the representative set of 329 two-chain complexes at various maximum target sequence coverage <i>q</i>_max.

<p>Percentage of alignments with full interface coverage (FIC alignments) in alignment pool produced by PSI-BLAST on the representative set of 329 two-chain complexes at various maximum target sequence coverage <i>q</i>_max.</p

Number of structures with full interface coverage alignments, <i>N</i>_FIC, for different types of complexes.

<p>Number of structures with full interface coverage alignments, <i>N</i>_FIC, for different types of complexes.</p

Examples of partial homology models.

<p>The models (white ribbons) are superimposed on the target native structures (gray ribbons). (A) Good accuracy model (interface RMSD = 5.0 Å) in the case of target and template proteins from the same organism. Target is malaria transmission blocking antibody 2A8 from mouse, (1z3g, chain H) and template is mouse BM3.3 T-cell receptor α-chain (1fo0, chain A). (B) Good accuracy model (interface RMSD = 3.7 Å) in the case of target and template proteins from different organisms. Target is guanine nucleotide-binding protein alpa-1 subunit from bovine, (1fqj, chain A) and template is yeast RAS-related protein RAB-33 (2g77, chain B). (C) Acceptable accuracy model (interface RMSD = 8.6 Å). Target is fibrillarin-like preRRNA processing protein from <i>Archaeoglobus fulgidus</i> (1nt2, chain A) and template is UDP-N-acetylglucosamine 4-epimerase from <i>Pseudomonas aeruginosa</i> (1sb8, chain A). (D) Incorrect model (interface RMSD = 16.9 Å). Target is human MHC Class II receptor HLA-DR1 (1kg0, chain B) and template is intron-encoded endonuclease from <i>Desulfurococcus mobilis</i> (1b24, chain A). Arrow indicates an incorrect loop which is the cause for large interface RMSD in this model. Blue and yellow meshes indicate positions of the backbone atoms of the interface residues in the model and the native structures, respectively. Other parameters of the models are presented in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000727#pcbi-1000727-t003" target="_blank">Table 3</a>.</p

Interacting chains with known structure used in calculations.

<p>First four symbols are the PDB code followed by the IDs of interacting chains as in the PDB file.</p

Distributions of interface identities and similarities in alignments containing all interface residues.

<p>Panels A and C show the distributions for the alignments with maximum query sequence coverage 40% and panels B and D show the distributions for the alignments irrespectively of query sequence coverage. For the definitions of interface identity and similarity see text.</p

Example of interface fragments corresponding to different cutoff values.

<p>Fragments of 1bp3 complex were extracted using interface cutoffs: (A) 6 Å, (B) 8 Å, (C) 10 Å, and (D) 12 Å. Ligand (the smaller protein in the complex) is in blue and Receptor (the larger protein in the complex) is in red.</p

Example of docking based on 12 Å and 16 Å interface libraries.

<p>3sic ligand (gray ribbons in A, B, D) was aligned with fragments of 1oyv ligand (red) extracted using 12 Å (A) and 16 Å (B) interface cutoffs. For comparison, the entire structure of 1oyv ligand is shown with 12 Å (C) and 16 Å (E) fragments (red). The entire structure of 3sic ligand with the loop participating in binding (blue) is shown in D. Binding loop in 3sic ligand is marked 1, and α-helix and β-sheet closest to this loop are marked 2 and 3, respectively.</p

Docking success rates for different interface libraries.

<p>The docking was performed on the Dockground benchmark set. The success rate is defined as percentage of target complexes for which at least one match is in top 10, top 100, and in all matches generated for the target has <i>i</i>-RMSD≤5, 8, and 10 Å. The results are shown for 6, 8, 10, 12, and 16 Å interface libraries (see the text for details).</p