Figure 2

Recognition of interface similarity across unrelated interfaces by PCalign and Ialign. The comparison is based on two geometric criteria; fraction of aligned residues (coverage) and RMSD of aligned residues. (A) All-against-all pairwise comparison, with PCalign (Ialign) aligning on average 53.1 ± 13.3% (51.4 ± 13.8%) of residues with RMSD of 3.725 ± 0.371 Å (3.810 ± 0.473 Å). (B) All-against-all pairwise comparison, with PCalign (Ialign) aligning on average 54.8 ± 13.2% (51.4 ± 13.8%) of residues with RMSD of 3.686 ± 0.378 Å (3.810 ± 0.473 Å), where the chemical term in PCalign is turned off to capture geometric similarity only. (C) Closest unrelated interface in the set of 124 dimers, with PCalign (Ialign) aligning on average 68.4 ± 14.5% (68.3 ± 15.6%) of residues with RMSD of 3.483 ± 0.366 Å (3.563 ± 0.502 Å). (D) Closest unrelated interface in the set of 124 dimers, with PCalign (Ialign) aligning on average 70.1 ± 15.4% (68.3 ± 15.6%) of residues with RMSD of 3.466 ± 0.371 Å (3.563 ± 0.502 Å), considering the geometric part of the scoring function in PCalign only. In all scenarios, PCalign does slightly better than Ialign in recognizing geometric similarities across unrelated interfaces, and using a scoring function that considers both chemical and geometric properties in PC-score performs less well compared to using one that considers purely geometric properties in PC-score, due to the fact that this analysis uses purely geometric criteria.