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Peer-Reviewed Publication
J Chem Theory Comput2026;22(4):1823-1833.February 24, 2026Journal Article

Boltz-ABFE: Free Energy Perturbation without Crystal Structures.

Stephan Thaler1,2, Zhiyi Wu2, William G Glass2, Richard T Bradshaw2, Gail Bartlett2, Prudencio Tossou1,2, Geoffrey P F Wood2
1Valence Laboratories, 6666 Rue Saint-Urbain 100, Montréal QC H2S 3H1, Canada.
2Recursion Pharmaceuticals Inc, Salt Lake City, Utah 84101, United States.
PubMed DOI

Abstract

Free energy perturbation (FEP) is considered the gold-standard simulation method for estimating small molecule binding affinity, a quantity of vital importance to drug discovery. The accuracy of FEP critically depends on an accurate model of the protein-ligand complex as an initial condition for the underlying molecular dynamics simulation. This requirement has limited the impact of FEP in earlier…

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