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. (PDF)

表A——不同晶体结构中测得的蛋白质天然界面（Native interface）尺寸，以及HADDOCK中用于定义建模模糊约束、驱动对接建模的对接界面（Docking interface）尺寸。本次计算基于97个成功对接的案例完成。
表B——蛋白质结合态与游离态之间的界面均方根偏差（Interface-RMSD），以及各案例中HADDOCK生成的最接近蛋白质结合态的模型与该结合态之间的界面均方根偏差（i-RMSD）。
表C——蛋白质-肽复合物标识符列表，及其对应的游离态复合物（若有）。本研究新增至PeptiDB的条目以红色标注。
图A——可接受模型对应的基准案例占比（即成功率）随配体-界面均方根偏差截断值的变化曲线。本分析中，若400个经水分子精修的模型中至少生成一个符合配体-界面均方根偏差截断值定义的可接受模型，则该次对接运行视为成功。
图B——采用默认HADDOCK对接协议的结合态-结合态对接性能。左面板展示了各对接阶段（刚性体对接it0、半柔性对接it1、水分子精修water）中近天然模型与亚埃级分辨率模型的占比（详见方法部分）。右面板则展示了经水分子精修后，模型占比随对接难度等级的变化情况。（PDF格式）