ArticleNature communications2025
Accelerating fragment-based drug discovery using grand canonical nonequilibrium candidate Monte Carlo.
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 2 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
2 citing papers in PubMed.
- Molecular Dynamics Workflows to Compute Large-Scale Sets of Absolute Binding Free Energies Aiding Drug Candidate and Binding Pose Selection.Journal of chemical theory and computation · 2026Article
- Advancing Medicinal Chemistry Through FMO: Sygnature's Platform.Methods in molecular biology (Clifton, N.J.) · 2026Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
Fragment-based drug discovery is a popular approach in the early stages of drug development. Computational tools are integral to these campaigns, providing a route to library design, virtual screening, the identification of putative small-molecule binding sites, the elucidation of binding geometries, and the prediction of accurate binding affinities. In this context, molecular dynamics-based simulations are increasingly popular, but often limited by sampling issues. Here, we develop grand canonical nonequilibrium candidate Monte Carlo (GCNCMC) to overcome these limitations. GCNCMC attempts the insertion and deletion of fragments to, or from, a region of interest; each proposed move is subject to a rigorous acceptance test based on the thermodynamic properties of the system. We demonstrate that fragment-based GCNCMC efficiently finds occluded fragment binding sites and accurately samples multiple binding modes. Finally, binding affinities of fragments are successfully calculated without the need for restraints, the handling of multiple binding modes, or symmetry corrections.
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Registered trials
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