Fig. 2

Optimization of the docking box size for Vina using the PDB-bench dataset. Docking accuracy assessed by (a) the RMSD over ligand heavy atoms, (b) the fraction of recovered binding residues, and (c) the fraction of recovered protein-ligand contacts, is plotted as a function of the ratio of the ligand radius of gyration to the box size. The corresponding docking accuracy using the default search space is shown on the right. Squares represent the mean values for each metric and whiskers show the standard deviation. The results obtained for experimental binding sites (black squares) are compared to those predicted by eFindSite (gray squares)