Professor Bert de Groot
Computational Biomolecular Dynamics Group
Max Planck Institute for Biophysical Chemistry
Goettingen, Germany

Tuesday, October 20, 2020
11:00 am (CT)
Zoom webinar recording

Abstract

Alchemical free energies form a powerful computational tool for the accurate prediction of stability changes due to mutation or relative ligand-receptor binding affinities. A non-equilibrium protocol facilitated by the PMX software will be presented for the efficient computation of such alchemical free energy changes, making use of thermodynamic cycles. A large-scale mutation scan will be presented on thermostability estimates due to point mutations in proteins, reaching an unprecedented accuracy thanks to a consensus force field approach. In addition, the affect of nucleic acid mutations on the affinity of protein-DNA complex will be presented. Finally, a protocol will be introduced for the efficient and accurate computation of relative affinities between receptors and drug-like ligands, for a set of 482 ligans pairs binding to 13 different receptors.