Bert de Groot

Max Planck Institute for Multidisciplinary Sciences, Goettingen, Germany

Alchemical binding free energy calculations for ligand binding, protein allostery, post-translational modifications, and more

Abstract

Alchemical free energy calculations have come of age. These calculations explore physical paths not experimentally accessible and provide unprecedented accuracy in the prediction of processes as diverse as protein thermostability and ligand binding free energies. Based on the PMX framework coupled to the GROMACS molecular dynamics engine, results of high-throughput relative as well as absolute ligand binding free energies are presented, in addition to applications of allostery in a GPCR and the effect of post-translational modifications in protein aggregation.