Quantum Mechanics/Molecular Mechanics Strategies for Docking Pose Refinement: Distinguishing between Binders and Decoys in Cytochrome c Peroxidase

We investigate the effect of systematically applying molecular dynamics (MD) and quantum mechanics/molecular mechanics (QM/MM) to docked poses in an attempt to improve the correspondence between theoretical prediction and experimental observation. The proposed scheme involves running a short time scale MD simulation on a docked ligand pose (and any known structurally important crystal structure waters in the active site), followed by QM/MM …