Fig. 8.

The issue of redundancy in ligand binding site prediction. A A set of predictions where 6/10 predictions are redundant, resulting in a low recall (1/5) and inflated precision (7/7) considering the top-N+2 predictions; B when redundancy is removed, only four predictions remain and recall increases to 3/5 (60%) and precision decreases to 3/4 (75%); C predictions by VN-EGNN, IF-SitePred and PUResNet, on chain D of PDB: 4Z9M [88], where ADP binds. For this ADP binding site, VN-EGNN reports 7 predictions, IF-SitePred 33, and PUResNet a single prediction. These three methods correctly predict this site, however, VN-EGNN and IF-SitePred report redundant pocket predictions, which centroids are very close in space (≤ 5 Å) and residues overlap considerably (≥ 0.75)