Fragment Pose Prediction Using Non-equilibrium Candidate Monte Carlo and Molecular Dynamics Simulations.

ABSTRACT: Part of early stage drug discovery involves determining how molecules may bind to the target protein. Through understanding where and how molecules bind, chemists can begin to build ideas on how to design improvements to increase binding affinities. In this retrospective study, we compare how computational approaches like docking, molecular dynamics (MD) simulations, and a non-equilibrium candidate Monte Carlo (NCMC)-based method (NCMC + MD) perform in predicting binding modes for a set of 12 fragment-like molecules, which bind to soluble epoxide hydrolase. We evaluate each method's effectiveness in identifying the dominant binding mode and finding additional binding modes (if any). Then, we compare our predicted binding modes to experimentally obtained X-ray crystal structures. We dock ea

SUBMITTER: Lim NM 

PROVIDER: S-EPMC7325745 | biostudies-literature | 2020 Apr

REPOSITORIES: biostudies-literature