File S1 - A Unified Conformational Selection and Induced Fit Approach to Protein-Peptide Docking

Table A - Size of the protein interface measured in the different crystal structures (Native interface) and respective size of the surface used to define ambiguous restraints in HADDOCK to drive the modeling (Docking interface). Calculations have been done over the 97 cases successfully docked. Table B - Interface-RMSD between bound and unbound forms of the proteins and i-RMSD between the closest model generated by HADDOCK and the bound form of the protein for each case. Table C - List of protein-peptide complexes identifiers with their corresponding free forms when available. In red, the new entries added to PeptiDB in this study. Figure A - Success rate (% of benchmark cases with acceptable models) as a function of the ligand-interface RMSD cutoff. In this analysis, a docking run is defined as successful if at least one acceptable model (as defined by the l-i-RMSD cutoff) is generated among the 400 water-refined models. Figure B - Bound/bound docking performance using the default HADDOCK protocol. The percentages of near-native and sub-angstrom resolution models (see Methods) at the various stages (rigid-body - it0, semi-flexible - it1 and water refinement - water) are reported in the left panels. The right panels show the percentages after water refinement as a function of the docking difficulty level.
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