Fig. 2.

Distinct ligands that bind to a given target protein often adopt similar binding poses and do so more frequently than predicted by a state-of-the-art per-ligand docking method. (A) Chemically distinct ligands share key interactions with the mineralocorticoid receptor (Protein Data Bank IDs: 2AA2, 5L7E, and 5MWP). (B) Across a set of 3,115 ligand pairs, interaction similarities are generally higher in pairs of correct poses than in pairs of poses ranked highly by a per-ligand scoring function. Shading depicts the per-target SEM. A.U.: arbitrary units. (C) Across a set of 690 ligand pairs with a shared substructure, the substructure tends to be placed more similarly in correct poses than in other poses ranked highly by a per-ligand scoring function (SI Appendix, Supplementary Text).