Pre-Exascale Computing of Protein–Ligand Binding Free Energies with Open Source Software for Drug Design
Vytautas Gapsys, David F. Hahn, Gary Tresadern, David L. Mobley, Markus Rampp, Bert L. de Groot
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.
Topics & Concepts
Leverage (statistics)WorkflowComputer scienceSoftwareExascale computingMolecular dynamicsLigand (biochemistry)Drug discoveryOpen source softwareComputational scienceOpen sourceChemistrySupercomputerComputational chemistryOperating systemDatabaseArtificial intelligenceReceptorBiochemistryProtein Structure and DynamicsComputational Drug Discovery MethodsMachine Learning in Materials Science