ArticleJournal of chemical information and modeling2025
FE-ToolKit: A Versatile Software Suite for Analysis of High-Dimensional Free Energy Surfaces and Alchemical Free Energy Networks.
Article in Journal of chemical information and modeling, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
What it found
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Who cites it
5 citing papers in PubMed.
- Origins of Reactivity in SAM-Utilizing Ribozyme SAMURI-Catalyzed RNA Alkylation.Journal of the American Chemical Society · 2026Article
- Large-Scale Collaborative Assessment of Binding Free Energy Calculations for Drug Discovery Using OpenFE.Journal of chemical information and modeling · 2026Article
- Automated Force Field Developer and Optimizer Platform: Torsion Reparameterization.Journal of chemical information and modeling · 2026Article
- A Relative Binding Free Energy Framework for Structurally Dissimilar Molecules.Journal of chemical information and modeling · 2026Article
- Recent Developments in Amber Biomolecular Simulations.Journal of chemical information and modeling · 2025Article
Corrections and comments
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Authors and funding
8 authors.
Funding
Abstract
Free energy simulations play a pivotal role in diverse biological applications, including enzyme design, drug discovery, and biomolecular engineering. The characterization of high-dimensional free energy surfaces underlying complex enzymatic mechanisms necessitates extensive sampling through umbrella sampling or string method simulations. Accurate ranking of target-binding free energies across large ligand libraries relies on comprehensive alchemical free energy calculations organized into thermodynamic networks. The predictive accuracy of these methods hinges on robust, scalable tools for networkwide data analysis and extraction of physical properties from heterogeneous simulation data. Here, we introduce FE-ToolKit, a versatile software suite for the automated analysis of free energy surfaces, minimum free energy paths, and alchemical free energy networks (thermodynamic graphs).
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.