3 papers
physics.bio-ph2025
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…
physics.chem-ph2023
Machine-learned molecular mechanics force field for the simulation of protein-ligand systems and beyond
Kenichiro Takaba, Iván Pulido, Pavan Kumar Behara +11
The development of reliable and extensible molecular mechanics (MM) force fields -- fast, empirical models characterizing the potential energy surface of molecular systems -- is in…