289 citations · 340 across the 6 of their papers we have counts for
6 papers
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…
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…
Precise binding free energy calculations for multiple molecules using an optimal measurement network of pairwise differences
Pengfei Li, Zhijie Li, Yu Wang +4
Alchemical binding free energy (BFE) calculations offer an efficient and thermodynamically rigorous approach to in silico binding affinity predictions. As a result of decades of me…
Best Practices for Alchemical Free Energy Calculations
Antonia S. J. S. Mey, Bryce Allen, Hannah E. Bruce Macdonald +11
Alchemical free energy calculations are a useful tool for predicting free energy differences associated with the transfer of molecules from one environment to another. The hallmark…
Optimal measurement network of pairwise differences
Huafeng Xu
When both the difference between two quantities and their individual values can be measured or computational predicted, multiple quantities can be determined from the measurements…
Molecular simulations minimally restrained by experimental data
Huafeng Xu
One popular approach to incorporating experimental data into molecular simulations is to restrain the ensemble average of observables to their experimental values. Here I derive eq…