Induced fit docking workflow based on charmm-gui modules: LBS Finder & Refiner and High-Throughput Simulator

Abstract

Molecular docking is a preferred method to predict ligand binding modes and their binding energy to target protein receptors, which is a critical first step in the early phase structure-based drug discovery. However, there is a persistent problem in docking that can be attributed to the induced fit effect, where the receptor binding site undergoes induced fit conformational changes upon ligand binding to achieve the correct binding mode. To solve this problem, we present a reliable stepwise docking workflow based on CHARMM-GUI LBS Finder & Refiner and High-Throughput Simulator.