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Peer-Reviewed Publication
J Chem Theory Comput2025;21(17):8330-8340.September 9, 2025Journal Article

Optimizing Absolute Binding Free Energy Calculations for Production Usage.

Zhiyi Wu1, Gerhard Konig1, Stefan Boresch2, Benjamin P Cossins3
1Recursion, Schrodinger Building, Oxford OX4 4GE, U.K.
2Faculty of Chemistry, Institute of Computational Biological Chemistry, University Vienna, Währinger Str. 17, Vienna 1090, Austria.
3Exscientia plc, Schrodinger Building, Oxford OX4 4GE, U.K.
PubMed DOI

Abstract

Protein-ligand binding affinity prediction is a key aspect in computational small molecule drug discovery. Several recent studies have demonstrated that molecular simulations based on alchemical absolute binding free-energy (ABFE) calculations are an accurate and broadly applicable tool for this purpose. However, the use of current ABFE protocols in large scale drug discovery projects occasionally…

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