Binding site prediction with closeness. Positive predicted value (PPV) of binding site predictions based on closeness parameter, considering only the residues with the top four closeness scores that were above the cutoff value indicated in abscissas. Random PPV is shown for comparison. The percentage of proteins that have any residue with a closeness value above the cutoff is shown ("% cases"). Data calculated for (A) all proteins in benchmark 3.0; (B) only enzyme/inhibitor cases (20.2% of the benchmark); (C) only "other" cases (51.6% of the benchmark); (D) only antibody/antigen cases (28.2% of the benchmark).