Jared M Sampson, Daniel A Cannon, Jianxin Duan, Jordan C K Epstein, Alina P Sergeeva, Phinikoula S Katsamba, Seetha M Mannepalli, Fabiana A Bahna, Hélène Adihou, Stéphanie M Guéret, Ranganath Gopalakrishnan, Stefan Geschwindner, D Gareth Rees, Anna Sigurdardottir, Trevor Wilkinson, Roger B Dodd, Leonardo De Maria, Juan Carlos Mobarec, Lawrence Shapiro, Barry Honig, Andrew Buchanan, Richard A Friesner, Lingle Wang
UNLABELLED: Computational free energy-based methods have the potential to significantly improve throughput and decrease costs of protein design efforts. Such methods must reach a high level of reliability, accuracy, and automation to be effectively deployed in practical industrial settings in a way that impacts protein design projects. Here, we present a benchmark study for the calculation of relative changes in protein-protein binding affinity for single point mutations across a variety of systems from the literature, using free energy perturbation (FEP+) calculations...
April 24, 2024: bioRxiv