33 citations · 70 across the 13 of their papers we have counts for
17 papers
Relative Binding Free Energy Estimation of Congeneric Ligands and Macromolecular Mutants with the Alchemical Transfer with Coordinate Swapping Method
Emilio Gallicchio
We present the Alchemical Transfer with Coordinate Swapping (ATS) method to enable the calculation of the relative binding free energies between large congeneric ligands and single…
Potential Distribution Theory of Alchemical Transfer
Solmaz Azimi, Emilio Gallicchio
We present an analytical description of the Alchemical Transfer Method (ATM) for molecular binding using the Potential Distribution Theory (PDT) formalism. ATM models the binding f…
Binding Selectivity Analysis from Alchemical Receptor Hopping and Swapping Free Energy Calculations
Solmaz Azimi, Emilio Gallicchio
We present receptor hopping and receptor swapping free energy estimation protocols based on the Alchemical Transfer Method (ATM) to model the binding selectivity of a set of ligand…
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…