2 papers
physics.comp-ph2025
Boltz-ABFE: Free Energy Perturbation without Crystal Structures
Stephan Thaler, Zhiyi Wu, William G. Glass +3
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. T…
physics.comp-ph2024
An evaluation of machine learning/molecular mechanics end-state corrections with mechanical embedding to calculate relative protein-ligand binding free energies
Johannes Karwounopoulos, Mateusz Bieniek, Zhiyi Wu +4
The development of machine-learning (ML) potentials offers significant accuracy improvements compared to molecular mechanics (MM) because of the inclusion of quantum-mechanical eff…