ArticleThe journal of physical chemistry. B2025
Binding Free Energy Calculations Based on the Path Collective Variable along a String Pathway.
Article in The journal of physical chemistry. B, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.
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Who cites it
2 citing papers in PubMed.
- Assessing Molecular Dynamics in Predicting Aptamer-Ligand Binding Thermodynamics: Insights from the OTA Binding Aptamers.Journal of chemical information and modeling · 2026Article
- On Free Energy Calculations in Drug Discovery.Accounts of chemical research · 2025Article
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3 authors.
Funding
Abstract
Calculating the binding free energy of small drug-like molecules to a macromolecular receptor is one of the most important applications of molecular dynamics simulations. One computational approach (the "geometrical route") seeks to determine the binding free energy of a ligand by calculating the potential of mean force along a physical path corresponding to the dissociation of the ligand from its receptor. We show here that it is possible to rigorously map the entire ligand-receptor separation process onto a curvilinear separation pathway constructed from the string method and then sample the longitudinal and orthogonal order parameters defined from the Path Collective Variable (PCV) along this pathway to calculate the binding free energy. The theory is illustrated by computing the absolute binding free energy of a glycogen synthase kinase-3 beta (GSK-3β) inhibitor, and the results are compared with the result from a calculation based on the standard alchemical double decoupling approach.
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