Machine-learned molecular mechanics force field for the simulation of protein-ligand systems and beyond

5 code implementations • 13 Jul 2023 • Kenichiro Takaba, Iván Pulido, Pavan Kumar Behara, Chapin E. Cavender, Anika J. Friedman, Michael M. Henry, Hugo MacDermott Opeskin, Christopher R. Iacovella, Arnav M. Nagle, Alexander Matthew Payne, Michael R. Shirts, David L. Mobley, John D. Chodera, Yuanqing Wang

The development of reliable and extensible molecular mechanics (MM) force fields -- fast, empirical models characterizing the potential energy surface of molecular systems -- is indispensable for biomolecular simulation and computer-aided drug design.

Drug Discovery

Best Practices for Alchemical Free Energy Calculations

1 code implementation • 7 Aug 2020 • Antonia S. J. S. Mey, Bryce Allen, Hannah E. Bruce Macdonald, John D. Chodera, Maximilian Kuhn, Julien Michel, David L. Mobley, Levi N. Naden, Samarjeet Prasad, Andrea Rizzi, Jenke Scheen, Michael R. Shirts, Gary Tresadern, Huafeng Xu

Alchemical free energy calculations are a useful tool for predicting free energy differences associated with the transfer of molecules from one environment to another.