ArticleJournal of computational chemistry2018
Comparison of free-energy methods using a tripeptide-water model system.
Article in Journal of computational chemistry, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- Accelerated Enveloping Distribution Sampling to Probe the Presence of Water Molecules.Journal of chemical theory and computation · 2023Article
- Computational Tools for Accurate Binding Free-Energy Prediction.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Optimization of Alchemical Pathways Using Extended Thermodynamic Integration.Journal of chemical theory and computation · 2021Article
- Toward Automated Free Energy Calculation with Accelerated Enveloping Distribution Sampling (A-EDS).Journal of chemical information and modeling · 2020Article
- Water in protein hydration and ligand recognition.Journal of molecular recognition : JMR · 2019Review
- Comparison of free-energy methods using a tripeptide-water model system.Journal of computational chemistry · 2018Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
We investigate the ability of several free-energy calculation methods to combine two alchemical changes. We use Bennett acceptance ratio (BAR), thermodynamic integration (TI), extended TI (X-TI), and enveloping distribution sampling (EDS) to perturb a water molecule, which is restrained to an amino acid that is also being perturbed. In addition to these pairwise methods, we present two two-dimensional approaches, EDS-TI and two-dimensional TI (2D-TI). We compare feasibility, efficiency and usability of these methods in regard to our simple model system, which mimics the displacement of a water molecule in the active site of a protein on residue mutation. The correct treatment of structural water has been shown to greatly aid binding affinity calculations in some cases that remained elusive otherwise. This is of broad interest in, for example, drug design, and we conclude that thus far, the pairwise method BAR and also the newer X-TI remain the most suitable methods to treat this problem as long as few end states are involved. © 2018 Wiley Periodicals, Inc.
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