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

Overview

Journal J Chem Inf Model

Publisher American Chemical Society

Specialties Chemistry
Medical Informatics

Date 2021 Mar 9

PMID 33686853

Citations 10

Authors

Yunhui Ge

David F Hahn

David L Mobley

Affiliations

Soon will be listed here.

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.

Citing Articles

Broadening the Scope of Binding Free Energy Calculations Using a Separated Topologies Approach.

Baumann H, Dybeck E, McClendon C, Pickard 4th F, Gapsys V, Perez-Benito L J Chem Theory Comput. 2023; 19(15):5058-5076.

PMID: 37487138 PMC: 10413862. DOI: 10.1021/acs.jctc.3c00282.

Identifying and Overcoming the Sampling Challenges in Relative Binding Free Energy Calculations of a Model Protein:Protein Complex.

Zhang I, Rufa D, Pulido I, Henry M, Rosen L, Hauser K J Chem Theory Comput. 2023; 19(15):4863-4882.

PMID: 37450482 PMC: 11219094. DOI: 10.1021/acs.jctc.3c00333.

Novel Allosteric Effectors Targeting Human Transcription Factor TEAD.

Tarek Ibrahim M, Verkhivker G, Misra J, Tao P Int J Mol Sci. 2023; 24(10).

PMID: 37240355 PMC: 10219411. DOI: 10.3390/ijms24109009.

Computational Exploration of Licorice for Lead Compounds against Duffy Binding Protein Utilizing Molecular Docking and Molecular Dynamic Simulation.

Yasir M, Park J, Han E, Park W, Han J, Kwon Y Molecules. 2023; 28(8).

PMID: 37110591 PMC: 10141081. DOI: 10.3390/molecules28083358.

Identifying and overcoming the sampling challenges in relative binding free energy calculations of a model protein:protein complex.

Zhang I, Rufa D, Pulido I, Henry M, Rosen L, Hauser K bioRxiv. 2023; .

PMID: 36945557 PMC: 10028896. DOI: 10.1101/2023.03.07.530278.

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