Pre-Exascale Computing of Protein–Ligand Binding Free Energies with Open Source Software for Drug Design

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 ef...

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Bibliographic Details
Published in:Journal of chemical information and modeling 2022-03, Vol.62 (5), p.1172-1177
Main Authors: Gapsys, Vytautas, Hahn, David F, Tresadern, Gary, Mobley, David L, Rampp, Markus, de Groot, Bert L
Format: Article
Language:English
Subjects:
Binding
Computation
Drug Design
Free energy
Freeware
Letter
Ligands
Mathematical analysis
Molecular dynamics
Molecular Dynamics Simulation
Open source software
Protein Binding
Proteins
Public domain
Software
Software packages
Thermodynamics
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Summary: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.
ISSN:1549-9596
1549-960X
1549-960X
DOI:10.1021/acs.jcim.1c01445