Molecular Dynamics Simulation to Study Protein Conformation and Ligand Interaction

The field of molecular dynamics (MD) simulations has become indispensable today to studying the conformational flexibility and dynamics of proteins as well as protein–ligand complexes. The technique helps to replicate real-time biological events like macromolecular dynamics on a computational platform and allows us to understand the fold and conformational changes in the protein–ligand complex. In addition, MD simulations enable us to estimate the thermodynamics and kinetics associated with protein–ligand binding. In this chapter, we introduce the basics of MD simulations and the theoretical aspects of the simulations. Further, we describe the sequential steps in the process of MD simulation and the background information of the steps. The chapter also discusses ligand binding and conformational changes with the help of case studies. Though the field has advanced by leaps and bounds, there is still a necessity for better force fields and methods to accurately predict the free energy of binding. In summary, research focusing on force fields supported by advancements in computational power will help researchers have better insights into protein–ligand interactions and their conformations.