Protein–Ligand Interaction and Molecular Dynamics Simulation

Protein–ligand interactions are essential in biological processes and are key factors in drug design and discovery. Rational drug development requires an understanding of these interactions and also the dynamic behaviour of protein–ligand complexes at the atomic level. Computational methods for examining protein–ligand interactions are molecular docking and molecular dynamics (MD) simulation, providing insights into crucial amino acid residues involved in various interactions, conformational changes, binding mechanisms, etc. This chapter offers an overview of molecular docking and MD simulation and their detailed steps, parameters, and applications in drug design and discovery. This can contribute to the rational design of novel therapeutics with higher efficiency and specificity by facilitating our understanding of protein–ligand interactions, allosteric modulation, drug resistance mechanisms, influence of solvent effects, etc. Integration of these computational techniques with different experimental methodologies further improves our understanding of the complexities of protein–ligand interactions and will help discover next-generation novel therapeutic agents.