A review on principles of molecular docking and its application in drug discovery

Abstract

Molecular docking (MD) is a computational technique that provides structural information and binding affinity of protein-ligand complexes in its thermodynamically favored conformation. This aids researchers in identifying active ligands that form stable complexes upon binding with targeted proteins for high throughput virtual screening and potential biological activities. This article provides features of molecular docking along with its application, accuracy, drawbacks, and significance in drug discovery projects and is expected to fill up a much-needed knowledge gap in this area. MD is divided into 3 types: rigid, flexible, and covalent docking. MD applies search algorithms to analyze feasible ways of attaching with targets and a scoring function is applied to determine binding affinity. Thus, the desired structure of the ligand preferably fitting in the target is obtained. Due to the ability of analyzing ligand-protein molecular processes, MD has significantly aided in drug discovery and selected success stories are presented in this thesis as well.