Molecular dynamics analysis to evaluate docking pose prediction.

ABSTRACT: The accurate prediction of a ligand-protein complex structure is important for computer-assisted drug development. Although many docking methods have been developed over the last three decades, the success of binding structure prediction remains greatly limited. The purpose of this study was to demonstrate the usefulness of molecular dynamics (MD) simulation in assessing a docking pose predicted using a docking program. If the predicted pose is not unstable in an aqueous environment, MD simulation equilibrates the system and removes the ligand from the predicted position. Here we investigated two proteins that are important potential therapeutic targets: β2 adrenergic receptor (β2AR) and PR-Set7. While β2AR is rigid and its ligands are very similar to the template ligand (carazolol), PR-Se

SUBMITTER: Sakano T 

PROVIDER: S-EPMC5042163 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature