{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,1]],"date-time":"2025-10-01T16:25:05Z","timestamp":1759335905132,"version":"3.37.3"},"reference-count":8,"publisher":"Oxford University Press (OUP)","issue":"14","license":[{"start":{"date-parts":[[2020,11,2]],"date-time":"2020-11-02T00:00:00Z","timestamp":1604275200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"INCEPTION","award":["PIA\/ANR-16-CONV-0005"],"award-info":[{"award-number":["PIA\/ANR-16-CONV-0005"]}]},{"DOI":"10.13039\/100000884","name":"CRI","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000884","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Ecole Doctorale FIRE - Programme Bettencourt"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,8,4]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>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.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The method is available on GitHub and distributed as a pip package.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa925","type":"journal-article","created":{"date-parts":[[2020,10,20]],"date-time":"2020-10-20T19:13:55Z","timestamp":1603221235000},"page":"2064-2065","source":"Crossref","is-referenced-by-count":13,"title":["quicksom: Self-Organizing Maps on GPUs for clustering of molecular dynamics trajectories"],"prefix":"10.1093","volume":"37","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4664-754X","authenticated-orcid":false,"given":"Vincent","family":"Mallet","sequence":"first","affiliation":[{"name":"Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3528, C3BI, USR3756 , Paris 75015, France"},{"name":"Mines ParisTech, Paris-Sciences-et-Lettres Research University, Center for Computational Biology , Paris 75272, France"}]},{"given":"Michael","family":"Nilges","sequence":"additional","affiliation":[{"name":"Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3528, C3BI, USR3756 , Paris 75015, France"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2792-6084","authenticated-orcid":false,"given":"Guillaume","family":"Bouvier","sequence":"additional","affiliation":[{"name":"Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3528, C3BI, USR3756 , Paris 75015, France"}]}],"member":"286","published-online":{"date-parts":[[2020,11,2]]},"reference":[{"key":"2023061310291041600_btaa925-B1","doi-asserted-by":"crossref","first-page":"1490","DOI":"10.1093\/bioinformatics\/btu849","article-title":"An automatic tool to analyze and cluster macromolecular conformations based on self-organizing maps","volume":"31","author":"Bouvier","year":"2015","journal-title":"Bioinformatics"},{"key":"2023061310291041600_btaa925-B2","doi-asserted-by":"crossref","first-page":"1545","DOI":"10.1002\/jcc.21287","article-title":"CHARMM: the biomolecular simulation program","volume":"30","author":"Brooks","year":"2009","journal-title":"J. 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