Benchmark of FlexPepDock ab-initio.

Performance of peptide modeling onto Bound (A) and Unbound (B) protein receptor structures.The proteins in the benchmark are detailed in Table S1 (See Methods for more details).∫The start bb-RMSD and start φ/ψ RMSD refer to the distance between the initial peptide conformation at the beginning of the simulation and the native peptide backbone.†The best peptide backbone interface-RMSD among all 50,000 sampled models.‡The best peptide backbone interface-RMSD within the ten models representing the top clusters.*The best all-atom RMSD of any partial hexamer of the peptide, among the ten top ranking models.aPDBids in italics indicate complexes modeled also on the free receptor conformation (see Table 2).bPentamer.cComplexes described in accompanying Figures.