Work

A Benchmark of Electrostatic Method Performance in Relative Binding Free Energy Calculations

Year: 2021

Type: article

Abstract: Relative free energy calculations are fast becoming a critical part of early stage pharmaceutical design, making it important to know how to obtain the best performance with these calculations in applications that could span hundreds of calculations and molecules. In this work, we compared two different treatments of long-range electrostatics, Particle Mesh Ewald (PME) and Reaction Field (RF), in relative binding free energy calculations using a nonequilibrium switching protocol. We found simulations using RF achieve comparable results to those using PME but gain more efficiency when using CPU and similar performance using GPU. The results from this work encourage more use of RF in molecular simulations.

Source: Journal of Chemical Information and Modeling

DOI: 10.1021/acs.jcim.0c01424

Authors: Yunhui Ge, David F. Hahn, David L. Mobley

Institutions: University of California, Irvine, Janssen (Belgium)

Language: English

Topic: Computational Drug Discovery Methods

Subfield: Drug Discovery

Field: Pharmacology, Toxicology and Pharmaceutics

Domain: Life Sciences

Open Access status: green

Funders: National Institutes of Health, National Cancer Institute, National Institute of General Medical Sciences

Awards: Computational alchemy for molecular design and optimization, Open data-driven infrastructure for building biomolecular force fields for predictive biophysics and drug design, Cancer Center Support Grant