ArticleNature communications2025
Enhanced sampling of protein conformational changes via true reaction coordinates from energy relaxation.
Article in Nature communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
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Who cites it
4 citing papers in PubMed.
- Free-Energy Landscapes of HBV Hexamer Closure Reveal Key Structural Features of the Transition.Journal of chemical theory and computation · 2026Article
- Contact Cluster Modeling of Allosteric Communication in PDZ Domains.The journal of physical chemistry. B · 2026Review
- AI-Resolved Protein Energy Landscapes, Electrodynamics, and Fluidic Microcircuits as a Unified Framework for Predicting Neurodegeneration.International journal of molecular sciences · 2026Review
- Kinetics of Proton Transfer and String of Conformational Transformation for 4-Pyridone-3-carboxylic Acid Under External Electric Field.Molecules (Basel, Switzerland) · 2025Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
The bottleneck in enhanced sampling lies in finding collective variables that effectively accelerate protein conformational changes; true reaction coordinates that accurately predict the committor are the well-recognized optimal choice. However, identifying them requires unbiased natural reactive trajectories, which, paradoxically, require effective enhanced sampling. Using the generalized work functional method, we uncover that true reaction coordinates control both conformational changes and energy relaxation, enabling us to compute them from energy relaxation simulations. Biasing true reaction coordinates accelerates conformational changes and ligand dissociation in PDZ2 domain and HIV-1 protease by 10
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Registered trials
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