14 citations · 15 across the 4 of their papers we have counts for
5 papers
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…
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…
Application of the Alchemical Transfer and Potential of Mean Force Methods to the SAMPL8 Host-Guest Blinded Challenge
Solmaz Azimi, Joe Z. Wu, Sheenam Khuttan +3
We report the results of our participation in the SAMPL8 GDCC Blind Challenge for host-guest binding affinity predictions. Absolute binding affinity prediction is of central import…
Relative Binding Free Energy Calculations for Ligands with Diverse Scaffolds with the Alchemical Transfer Method
Solmaz Azimi, Sheenam Khuttan, Joe Z. Wu +2
We present an extension of Alchemical Transfer Method (ATM) for the estimation of relative binding free energies of molecular complexes applicable to conventional as well as scaffo…
Alchemical Transfer Approach to Absolute Binding Free Energy Estimation
Joe Z. Wu, Solmaz Azimi, Sheenam Khuttan +2
The Alchemical Transfer Method (ATM) for the calculation of standard binding free energies of non-covalent molecular complexes is presented. The method is based on a coordinate dis…