Molecular Dynamics Simulation of Proteins: A Brief Overview

Sachin Patodia, Ashima Baga

Abstract

MD simulation has become an essential tool for understanding the physical basis of the structure of proteins and their biological functions. During the current decade we witnessed significant progress in MD simulation of proteins with advancement in atomistic simulation algorithms, force fields, computational methods and facilities, comprehensive analysis and experimental validation, as well as integration in wide area bioinformatics and structural/systems biology frameworks. In this review, we present the methodology on protein simulations and recent advancements in the field. MD simulation provides a platform to study protein–protein, protein–ligand and protein–nucleic acid interactions. MD simulation is also done with NMR relaxation timescale in order to get residual dipolar coupling and order parameter of protein molecules.