FINDSITELHM: A Threading-Based Approach to Ligand Homology Modeling
Figure 4
Confidence index for ligand docking by FINDSITELHM.
Box and whiskers plots of the relationship between the accuracy FINDSITELHM in terms of the RMSD from the crystal ligand pose calculated for its heavy atoms and (A) the coverage of the anchor substructure by a target ligand, (B) the structural conservation of anchor binding mode expressed as the average pairwise RMSD (pRMSD) of the anchor functional groups, and (C) correlation between the pocket prediction accuracy by FINDSITE assessed by the distance between the predicted pocket center and the predicted center of mass of the native ligand. Boxes end at the quartiles Q1 and Q3; a horizontal line in a box is the median. Whiskers point at the farthest points within 1.5 times the interquartile range and circles represent the outliers.