ArticleThe Journal of chemical physics2025
Tutorial on quantifying and sampling biomolecular ensembles with ShapeGMM.
Article in The Journal of chemical physics, 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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2 citing papers in PubMed.
- The impact of glycosylation on the conformational ensembles of β-, δ-, and γ-sarcoglycans.Biophysical journal · 2026Article
- Mechanochemical Decoupling of ATP Hydrolysis and RNA Translocation in SARS-CoV-2 nsp13 by the L405D Mutation.bioRxiv : the preprint server for biology · 2026Article
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3 authors.
Funding
Abstract
Here, we present a detailed workflow for clustering and enhanced sampling of biomolecular conformations using the ShapeGMM methodology. This approach fits a probabilistic model of biomolecular conformations rooted in the idea that the free energy can be expressed in terms of local fluctuations in atomic positions around metastable states. We demonstrate using a single model system how to generate and fit equilibrium molecular dynamics simulation data. We then demonstrate how to use the resulting model to generate a reaction coordinate between two states, how to sample along that coordinate using metadynamics using our size-and-shape PLUMED module, and how to cluster those biased conformations to obtain a refined equilibrium ShapeGMM model.
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