Ligand Pose and Orientational Sampling in Molecular Docking
A) The crystal ligand from PDB Code 1VSO. The critical contacts are defined as 3 atoms from the ligand crystal structure making key polar contacts with the protein, highlighted with spheres. 4 poses of ZINC00013260 are shown in B through E, with increasing sampling going from left to right, better DOCK scores and lower critical contact RMSD (with the exception of the critical contact RMSD rising from Match Goal of 50 to 500). Protein is shown in gray, crystal ligand shown in purple and representative docked pose shown in green, with hydrogen bonds drawn according to UCSF Chimera defaults. An additional molecule, ZINC00374553, is similarly shown in subfigures F through I, with a similar trend of increasing DOCK energies and decreasing critical contact RMSD.