Ligand Pose and Orientational Sampling in Molecular Docking
The effect of changing the desired number of match goals, or orientational samples, on the overall enrichment of ligands over matched decoys is shown. Three possibilities are shown, A & C) MAP Kinase-Activated Protein Kinase 2 (MAPK2), where the logAUC goes down with increased orientational sampling, above that is the difference in DOCK energies for ligands and decoys for that target. B & D) Protein Farnesyltransferase/Geranylgeranyltransferase Type I Alpha Subunit (FNTA), where the logAUC does not change significantly with increased orientational sampling, again the difference between the ligand and decoy energies is shown above in the upper right. E), GRIK1 is shown, where the logAUC goes up with increased orientational sampling.