CHARMM‐GUIhigh‐throughput simulator for efficient evaluation of protein–ligand interactions with different force fields

Abstract

AbstractMolecular docking is one of the most popular computational tools for the hit discovery step in drug design. However, there is ample room for improvement of docking's ability to identify correct binding modes and discriminate active from decoy compounds. Molecular dynamics (MD) simulations of protein–ligand docking structures have been shown to be effective in improving docking results. Here, we present CHARMM‐GUI high‐throughput simulator (HTS) that prepares MD simulation systems and inputs for multiple protein–ligand complex structures in a high‐throughput manner. HTS supports commonly used MD programs (NAMD, GROMACS, AMBER, OpenMM, GENESIS, Desmond, LAMMPS, and Tinker) along with various force field combinations for protein and ligand, including CHARMM36m, Amber (ff19SB/ff14SB), OPLS‐AA/M, CGenFF, GAFF2, and OpenFF. Validation tests using Miller and the directory of useful decoys‐enhanced (DUD‐E) datasets demonstrate that short MD simulations using HTS‐generated systems and simple ligand RMSD calculations consistently outperform docking results. Specifically, MD simulations can better identify correct ligand‐binding modes among top 10 binding poses as compared to docking scores. In addition, MD simulations can better discriminate active from decoy compounds in the DUD‐E dataset than docking scores for both soluble and membrane proteins. We expect that HTS can be a useful tool to facilitate the hit discovery process in drug design by improving docking results.