{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,3]],"date-time":"2026-04-03T01:28:08Z","timestamp":1775179688165,"version":"3.50.1"},"reference-count":23,"publisher":"Oxford University Press (OUP)","issue":"23","license":[{"start":{"date-parts":[[2022,10,7]],"date-time":"2022-10-07T00:00:00Z","timestamp":1665100800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/pages\/standard-publication-reuse-rights"}],"funder":[{"name":"Cuban Oficina de Gesti\u00f3n de Fondos y Proyectos Internacionales","award":["PN223LH010-02"],"award-info":[{"award-number":["PN223LH010-02"]}]},{"name":"Eiffel Scholarship Program of Excellence of Campus France","award":["P104786Z"],"award-info":[{"award-number":["P104786Z"]}]},{"name":"Project Hubert Curien-Carlos J. Finlay","award":["41814TM"],"award-info":[{"award-number":["41814TM"]}]},{"DOI":"10.13039\/501100002850","name":"Fondo Nacional de Desarrollo Cient\u00edfico y Tecnol\u00f3gico","doi-asserted-by":"publisher","award":["1210138"],"award-info":[{"award-number":["1210138"]}],"id":[{"id":"10.13039\/501100002850","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,11,30]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>The term clustering designates a comprehensive family of unsupervised learning methods allowing to group similar elements into sets called clusters. Geometrical clustering of molecular dynamics (MD) trajectories is a well-established analysis to gain insights into the conformational behavior of simulated systems. However, popular variants collapse when processing relatively long trajectories because of their quadratic memory or time complexity. From the arsenal of clustering algorithms, HDBSCAN stands out as a hierarchical density-based alternative that provides robust differentiation of intimately related elements from noise data. Although a very efficient implementation of this algorithm is available for programming-skilled users (HDBSCAN*), it cannot treat long trajectories under the de facto molecular similarity metric RMSD.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Here, we propose MDSCAN, an HDBSCAN-inspired software specifically conceived for non-programmers users to perform memory-efficient RMSD-based clustering of long MD trajectories. Methodological improvements over the original version include the encoding of trajectories as a particular class of vantage-point tree (decreasing time complexity), and a dual-heap approach to construct a quasi-minimum spanning tree (reducing memory complexity). MDSCAN was able to process a trajectory of 1 million frames using the RMSD metric in about 21\u2009h with &amp;lt;8 GB of RAM, a task that would have taken a similar time but more than 32 TB of RAM with the accelerated HDBSCAN* implementation generally used.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The source code and documentation of MDSCAN are free and publicly available on GitHub (https:\/\/github.com\/LQCT\/MDScan.git) and as a PyPI package (https:\/\/pypi.org\/project\/mdscan\/).<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btac666","type":"journal-article","created":{"date-parts":[[2022,10,7]],"date-time":"2022-10-07T14:25:45Z","timestamp":1665152745000},"page":"5191-5198","source":"Crossref","is-referenced-by-count":17,"title":["MDSCAN: RMSD-based HDBSCAN clustering of long molecular dynamics"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3852-4902","authenticated-orcid":false,"given":"Roy","family":"Gonz\u00e1lez-Alem\u00e1n","sequence":"first","affiliation":[{"name":"Laboratorio de Qu\u00edmica Computacional y Te\u00f3rica (LQCT), Facultad de Qu\u00edmica, Universidad de La Habana , La Habana 10400, Cuba"},{"name":"Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Universit\u00e9 Paris Saclay , Gif-sur-Yvette F-91198, France"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6454-4320","authenticated-orcid":false,"given":"Daniel","family":"Platero-Rochart","sequence":"additional","affiliation":[{"name":"Laboratorio de Qu\u00edmica Computacional y Te\u00f3rica (LQCT), Facultad de Qu\u00edmica, Universidad de La Habana , La Habana 10400, Cuba"}]},{"given":"Alejandro","family":"Rodr\u00edguez-Serradet","sequence":"additional","affiliation":[{"name":"Laboratorio de Qu\u00edmica Computacional y Te\u00f3rica (LQCT), Facultad de Qu\u00edmica, Universidad de La Habana , La Habana 10400, Cuba"}]},{"given":"Erix W","family":"Hern\u00e1ndez-Rodr\u00edguez","sequence":"additional","affiliation":[{"name":"Laboratorio de Bioinform\u00e1tica y Qu\u00edmica Computacional, Departamento de Medicina Traslacional, Facultad de Medicina, Universidad Cat\u00f3lica del Maule , Talca 3480094, Chile"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0182-1444","authenticated-orcid":false,"given":"Julio","family":"Caballero","sequence":"additional","affiliation":[{"name":"Departamento de Bioinform\u00e1tica, Facultad de Ingenier\u00eda, Centro de Bioinform\u00e1tica, Simulaci\u00f3n y Modelado (CBSM), Universidad de Talca , Talca, Chile"}]},{"given":"Fabrice","family":"Leclerc","sequence":"additional","affiliation":[{"name":"Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Universit\u00e9 Paris Saclay , Gif-sur-Yvette F-91198, France"}]},{"given":"Luis","family":"Montero-Cabrera","sequence":"additional","affiliation":[{"name":"Laboratorio de Qu\u00edmica Computacional y Te\u00f3rica (LQCT), Facultad de Qu\u00edmica, Universidad de La Habana , La Habana 10400, Cuba"}]}],"member":"286","published-online":{"date-parts":[[2022,10,7]]},"reference":[{"key":"2022113016195100500_btac666-B1","doi-asserted-by":"crossref","first-page":"1000","DOI":"10.1109\/T-C.1975.224110","article-title":"An algorithm for finding nearest neighbors","volume":"C-24","author":"Baskett","year":"1975","journal-title":"IEEE Trans. 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