ArticleJournal of chemical information and modeling2021
A Benchmark of Electrostatic Method Performance in Relative Binding Free Energy Calculations.
Article in Journal of chemical information and modeling, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Integrative reverse vaccinology and computational modeling for the rational design of a broadly immunogenic multi-epitope vaccine against Marburg virus infection.Naunyn-Schmiedeberg's archives of pharmacology · 2026Article
- Advance biocatalyst for the green conversion of 5-hydroxymethylfurfural to a biopolymer precursor 2,5-furandicarboxylic acid.Biotechnology for biofuels and bioproducts · 2025Article
- Identifying and Overcoming the Sampling Challenges in Relative Binding Free Energy Calculations of a Model Protein:Protein Complex.Journal of chemical theory and computation · 2023Article
- Broadening the Scope of Binding Free Energy Calculations Using a Separated Topologies Approach.Journal of chemical theory and computation · 2023Article
- Identifying and overcoming the sampling challenges in relative binding free energy calculations of a model protein:protein complex.bioRxiv : the preprint server for biology · 2023Article
- Novel Allosteric Effectors Targeting Human Transcription Factor TEAD.International journal of molecular sciences · 2023Article
- Computational Exploration of Licorice for Lead Compounds againstMolecules (Basel, Switzerland) · 2023Article
- Prioritizing Small Sets of Molecules for Synthesis through in-silico Tools: A Comparison of Common Ranking Methods.ChemMedChem · 2023Article
- Absolute Binding Free Energy Calculations for Buried Water Molecules.Journal of chemical theory and computation · 2022Article
- Correction Schemes for Absolute Binding Free Energies Involving Lipid Bilayers.Journal of chemical theory and computation · 2022Article
- Expanded Ensemble Methods Can be Used to Accurately Predict Protein-Ligand Relative Binding Free Energies.Journal of chemical theory and computation · 2021Article
- Temperature artifacts in protein structures bias ligand-binding predictions.Chemical science · 2021Article
Corrections and comments
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Authors and funding
3 authors.
Funding
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.
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Registered trials
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