Fig. 7
From: Comparative evaluation of methods for the prediction of protein–ligand binding sites
Ligand binding site prediction benchmark at the residue level. DeepPocketRESC predictions are not included in the F1 and MCC analyses as these are re-scored and re-ranked fpocket predictions and the results would be the same as fpocket’s. A F1 score distributions; B MCC distributions. In both panels, each data point in the distribution corresponds to the score obtained from all residues in a protein chain; C mean ROC curve for methods that report a residue score. Dashed line represents the baseline, 1 FP for each TP, i.e., diagonal and AUC = 0.5; D mean PR curve. Dashed line represents the baseline, i.e., proportion of observed binding residues = 0.1; Mean ROC and PR curves are calculated by averaging the curves of the 2775 LIGYSIS protein chains. E Distribution of residue ligandability scores for IF-SitePred, GrASP and P2Ranks. PocketFinder+, Ligsite+ and Surfnet+ are not included as their scores do not range 0–1, and a small number of scores can reach values > 25. (d) indicates that these predictions originate from the original methods run with default parameters