ArticleBioinformatics (Oxford, England)2023
MDSubSampler: a posteriori sampling of important protein conformations from biomolecular simulations.
Article in Bioinformatics (Oxford, England), 2023. 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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Who cites it
2 citing papers in PubMed.
- MDGraphEmb: a toolkit for graph embedding and classification of protein conformational ensembles.Bioinformatics (Oxford, England) · 2025Article
- Cell phenotypes can be predicted from propensities of protein conformations.Current opinion in structural biology · 2023Review
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4 authors.
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Abstract
motivationMolecular dynamics (MD) simulations have become routine tools for the study of protein dynamics and function. Thanks to faster GPU-based algorithms, atomistic and coarse-grained simulations are being used to explore biological functions over the microsecond timescale, yielding terabytes of data spanning multiple trajectories, thereby extracting relevant protein conformations without losing important information is often challenging.
resultsWe present MDSubSampler, a Python library and toolkit for a posteriori subsampling of data from multiple trajectories. This toolkit provides access to uniform, random, stratified, weighted sampling, and bootstrapping sampling methods. Sampling can be performed under the constraint of preserving the original distribution of relevant geometrical properties. Possible applications include simulations post-processing, noise reduction, and structures selection for ensemble docking. AVAILABILITY AND IMPLEMENTATION: MDSubSampler is freely available at https://github.com/alepandini/MDSubSampler, along with guidance on installation and tutorials on how it can be used.
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