Molecular dynamics simulations in drug discovery

Official URL: https://dx.doi.org/10.1016/B978-0-323-95502-7.00273-6

Proteins are essential for cellular functions. At the atomic level, the proteins are in constant motion, and it is these movements in a controlled environment that provide important insights into their functions. Molecular dynamic (MD) simulations and related techniques enable time dependent capture of the positions and motion of every atom, which would otherwise be difficult using experimental technique. The chapter highlights how molecular dynamics improves accuracy of drug binding predictions, enhancing insights into structural dynamics and binding energies. Techniques like metadynamics aid in exploring complex protein states and cryptic binding pockets that are crucial for drug targeting. MD simulations also complement artificial intelligence (AI) models like AlphaFold, refining protein structure predictions for drug discovery despite some limitations.