quicksom: Self-Organizing Maps on GPUs for clustering of molecular dynamics trajectories

SUMMARY: We implemented the Self-Organizing Maps algorithm running efficiently on GPUs, and also provide several clustering methods of the resulting maps. We provide scripts and a use case to cluster macro-molecular conformations generated by molecular dynamics simulations. AVAILABILITY AND IMPLEMEN...

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Detalles Bibliográficos
Autores principales: Mallet, Vincent, Nilges, Michael, Bouvier, Guillaume
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2020
Materias:
Applications Notes
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8336998/
https://www.ncbi.nlm.nih.gov/pubmed/33135048
http://dx.doi.org/10.1093/bioinformatics/btaa925
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author Mallet, Vincent
Nilges, Michael
Bouvier, Guillaume
author_facet Mallet, Vincent
Nilges, Michael
Bouvier, Guillaume
author_sort Mallet, Vincent
collection PubMed
description SUMMARY: We implemented the Self-Organizing Maps algorithm running efficiently on GPUs, and also provide several clustering methods of the resulting maps. We provide scripts and a use case to cluster macro-molecular conformations generated by molecular dynamics simulations. AVAILABILITY AND IMPLEMENTATION: The method is available on GitHub and distributed as a pip package.
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spelling pubmed-83369982021-08-09 quicksom: Self-Organizing Maps on GPUs for clustering of molecular dynamics trajectories Mallet, Vincent Nilges, Michael Bouvier, Guillaume Bioinformatics Applications Notes SUMMARY: We implemented the Self-Organizing Maps algorithm running efficiently on GPUs, and also provide several clustering methods of the resulting maps. We provide scripts and a use case to cluster macro-molecular conformations generated by molecular dynamics simulations. AVAILABILITY AND IMPLEMENTATION: The method is available on GitHub and distributed as a pip package. Oxford University Press 2020-11-02 /pmc/articles/PMC8336998/ /pubmed/33135048 http://dx.doi.org/10.1093/bioinformatics/btaa925 Text en © The Author(s) 2020. Published by Oxford University Press. https://creativecommons.org/licenses/by-nc/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/ (https://creativecommons.org/licenses/by-nc/4.0/) ), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Applications Notes
Mallet, Vincent
Nilges, Michael
Bouvier, Guillaume
quicksom: Self-Organizing Maps on GPUs for clustering of molecular dynamics trajectories
title quicksom: Self-Organizing Maps on GPUs for clustering of molecular dynamics trajectories
title_full quicksom: Self-Organizing Maps on GPUs for clustering of molecular dynamics trajectories
title_fullStr quicksom: Self-Organizing Maps on GPUs for clustering of molecular dynamics trajectories
title_full_unstemmed quicksom: Self-Organizing Maps on GPUs for clustering of molecular dynamics trajectories
title_short quicksom: Self-Organizing Maps on GPUs for clustering of molecular dynamics trajectories
title_sort quicksom: self-organizing maps on gpus for clustering of molecular dynamics trajectories
topic Applications Notes
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8336998/
https://www.ncbi.nlm.nih.gov/pubmed/33135048
http://dx.doi.org/10.1093/bioinformatics/btaa925
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AT bouvierguillaume quicksomselforganizingmapsongpusforclusteringofmoleculardynamicstrajectories

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