38 citations · 118 across the 16 of their papers we have counts for
4 papers · 1 filter
What to Make of Zero: Resolving the Statistical Noise from Conformational Reorganization in Alchemical Binding Free Energy Estimates with Metadynamics Sampling
Sheenam Khuttan, Emilio Gallicchio
We introduce the self-Relative Binding Free Energy (self-RBFE) approach to evaluate the intrinsic statistical variance of dual-topology alchemical binding free energy estimators. T…
Performance and Analysis of the Alchemical Transfer Method for Binding Free Energy Predictions of Diverse Ligands
Lieyang Chen, Yujie Wu, Chuanjie Wu +4
The Alchemical Transfer Method (ATM) is herein validated against the relative binding free energies of a diverse set of protein-ligand complexes. We employed a streamlined setup wo…
Validation of the Alchemical Transfer Method for the Estimation of Relative Binding Affinities of Molecular Series
Francesc Sabanés Zariquiey, Adrià Pérez, Maciej Majewski +2
The accurate prediction of protein-ligand binding affinities is crucial for drug discovery. Alchemical free energy calculations have become a popular tool for this purpose. However…
Taming Multiple Binding Poses in Alchemical Binding Free Energy Prediction: the -cyclodextrin Host-Guest SAMPL9 Blinded Challenge
Sheenam Khuttan, Solmaz Azimi, Joe Z. Wu +4
We apply the Alchemical Transfer Method (ATM) and a bespoke fixed partial charge force field to the SAMPL9 bCD host-guest binding free energy prediction challenge that comprises a…