Molecular Docking and Dynamics in Computer-Aided Drug Design

Abstract

Applying computational methods to biological data is the focus of the interdisciplinary field of bioinformatics. One of the most important applications of bioinformatics is in the field of drug discovery, where researchers use computer simulations to predict the binding of a drug molecule to a protein target. Two commonly used techniques for this purpose are docking and molecular dynamics simulation. For the past twenty years, methods for computer-aided drug design have been used in the field of drug development. The use of computer resources in molecular dynamics, docking, and simulation techniques required a solid understanding of the receptor-ligand interaction mechanism. The docking studies approach's main goal is to determine whether two or even more molecular structures—such as proteins, enzymes, nucleic, and tiny leads or drugs—fit together. In order to anticipate the ligand's orientation and binding affinity in the target protein's active site, protein- ligand (small molecule), protein-nucleic acid, and protein-protein docking are crucial. Bioinformatics researchers use both docking and molecular dynamics simulation techniques to understand the interactions between drugs and protein targets, with the ultimate goal of designing more effective and efficient drugs. In the pharmaceutical sector, these methods are often employed and have become a crucial component of the drug development process.