Pre-exascale computing of protein–ligand binding free energies with open source 
software for drug design

Gapsys, Vytautas; Hahn, David F.; Tresadern, Gary; Mobley, David L.; Rampp, Markus; de Groot, and Bert L.

doi:10.1021/acs.jcim.1c01445

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Pre-exascale computing of protein–ligand binding free energies with open source software for drug design

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Rampp, Markus
Max Planck Computing and Data Facility, Max Planck Society;

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Citation

Gapsys, V., Hahn, D. F., Tresadern, G., Mobley, D. L., Rampp, M., & de Groot, a. B. L. (2022). Pre-exascale computing of protein–ligand binding free energies with open source software for drug design. Journal of Chemical Information and Modeling, 62(5), 1172-1177. doi:10.1021/acs.jcim.1c01445.

Cite as: https://hdl.handle.net/21.11116/0000-000A-21ED-6

Abstract

Nowadays, drug design projects benefit from highly accurate protein–ligand binding free energy predictions based on molecular dynamics simulations. While such calculations have been computationally expensive in the past, we now demonstrate that workflows built on open source software packages can efficiently leverage pre-exascale computing resources to screen hundreds of compounds in a matter of days. We report our results of free energy calculations on a large set of pharmaceutically relevant targets assembled to reflect industrial drug discovery projects.