2 papers
physics.bio-ph2026
Improving sampling of binding free energy differences between covalently bound ligands in alternate binding pockets using MT-REXEE
Anika J. Friedman, Jerome M. Fox, Michael R. Shirts
The primary limitation for the application of alchemical free energy methods to a wider variety of complex molecular systems is achieving reasonable sampling. Flexible binding comp…
physics.chem-ph2024
Multiple Topology Replica Exchange of Expanded Ensembles (MT-REXEE) for Multidimensional Alchemical Calculations
Anika J. Friedman, Wei-Tse Hsu, Michael R. Shirts
Relative free energy calculations are now widely used in academia and industry, but the accuracy is often limited by poor sampling of the complexes conformational ensemble. To addr…