Fig. 2. CovPepDock is successful in retrospective benchmarks. (A) Percent of starting structures in the disulfides dataset, for which a near-native model (interface backbone RMSD < 2 Å) was sampled (light blue), ranked among the top five scoring models (blue) or ranked as the top scoring model (dark blue). Similarly, (B) shows the percent of sub-angstrom models (interface backbone RMSD < 1 Å) in the disulfides dataset. (C) Native conformation (cyan) and top-scoring model (magenta) of PDB ID 5FGY from the disulfides dataset. (D) and (E) Show the percent of near-native models and sub-angstrom models in the electrophiles dataset, accordingly, and (F) shows the docking prediction for PDB ID 4WVI from the electrophiles dataset.