Drug Design in Motion: Concepts and Applications of Classical Molecular Dynamics Simulations

Molecular dynamics (MD) simulations have transformed the landscape of drug design, being one of the first computational techniques to provide insights into the behaviour of biomolecules at the atomic level. Nowadays, MD play a crucial role in predicting ligand binding affinities, exploring the protein–ligand complexes, facilitating drug binding studies, understanding protein–protein interactions, and discovering structural states and binding sites. The integration of MD simulations with experimental techniques accelerates the identification and optimisation of potential drug candidates. In this chapter, we discuss applications of MD simulations that cover a wide range of possibilities within in silico drug design. Among others are the docking postprocessing of protein–ligand complexes, drug binding studies, protein–protein interactions, and the discovery of structural states and binding sites.