Success rates for unbound docking using DrugScorePPI/FRODOCK and the original FRODOCK implementation.[a]

[a]Docking calculations were performed for a subset of 96 structures of the ZDOCK benchmark 3.0 (see Materials and Methods section). The percentage of complexes is reported for which at least one solution with the given accuracy was found in the top 1, 10, and 100 solutions. The “Top 2000” column reports the percentage of complexes for which at least one solution with the given accuracy was found in the top 2000 solutions. In neither docking approach was a high accuracy solution found.[b]A global search of ligand configurations around the receptor was performed as in the case of bound docking.[c]The search space for the knowledge-driven docking was restricted to 10 Å around a central point. For details, see Figure S3 in File S1. The mean is reported for three independent docking runs. The standard deviation is ≤ 2.2 in all cases.