Fig. 3: Relationship between BiSyRMSD and LDDT-PLI.

a, A scatter plot of LDDT-PLI (x axis) and BiSyRMSD (y axis, log scale). Each point (n = 31,905) represents an assigned reference ligand pair. Pairs for which LDDT-PLI (n = 7,798) or BiSyRMSD (n = 7,921) could not be computed are represented with a triangle and values were replaced with −0.1 (LDDT-PLI) or a value of 1.5 times the highest BiSyRMSD score observed in the analysis. Points have 10% opacity, and more solid points indicate multiple identical predictions. Interesting outliers are marked with arrows. b–d, Examples of ligand outlier pose predictions with disagreeing LDDT-PLI and BiSyRMSD models highlighted in a, showing flipped side chains (b), a disconnected ligand (c) and misplaced ion conserving inter-atomic distances (d). Model chains are depicted in purple and reference chains in green. Binding site residues and ligands are shown as balls and sticks.