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Updated: Oct 2, 2025

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
Published on: June 20, 2025
Pre-Exascale Computing of Protein-Ligand Binding Free Energies with Open Source Software for Drug Design
Vytautas Gapsys1, David F Hahn2, Gary Tresadern2
1Computational Biomolecular Dynamics Group, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.
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.
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