ArticlebioRxiv : the preprint server for biology2025
Tutorial on quantifying and sampling biomolecular ensembles with ShapeGMM.
Article in bioRxiv : the preprint server for biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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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 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 show 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 give a refined equilibrium ShapeGMM model.
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