Molecular dynamics simulations for the protein–ligand complex structures obtained by computational docking studies using implicit or explicit solvents

Abstract Computational docking programs generally predict many candidates for ligand poses, and only one or few poses should be selected for later drug design. In this study, we performed molecular dynamics (MD) simulations on 81 test sets of protein–ligand complexes and determined how well MD simulations evaluated docking poses. Our results suggest that appropriate candidate poses can be chosen from the many docking poses by using MD simulations with explicit solvents. To distinguish the appropriate pose from other candidates, 5-ns and 10-ns MD simulations were effective.