{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,27]],"date-time":"2025-10-27T11:00:47Z","timestamp":1761562847140,"version":"3.37.3"},"reference-count":26,"publisher":"Oxford University Press (OUP)","issue":"7","license":[{"start":{"date-parts":[[2022,1,10]],"date-time":"2022-01-10T00:00:00Z","timestamp":1641772800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Eiffel Scholarship Program of Excellence of Campus France","award":["P744468L"],"award-info":[{"award-number":["P744468L"]}]},{"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":["3170107"],"award-info":[{"award-number":["3170107"]}],"id":[{"id":"10.13039\/501100002850","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,3,28]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Density Peaks is a widely spread clustering algorithm that has been previously applied to Molecular Dynamics (MD) simulations. Its conception of cluster centers as elements displaying both a high density of neighbors and a large distance to other elements of high density, particularly fits the nature of a geometrical converged MD simulation. Despite its theoretical convenience, implementations of Density Peaks carry a quadratic memory complexity that only permits the analysis of relatively short trajectories.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Here, we describe DP+, an exact novel implementation of Density Peaks that drastically reduces the RAM consumption in comparison to the scarcely available alternatives designed for MD. Based on DP+, we developed RCDPeaks, a refined variant of the original Density Peaks algorithm. Through the use of DP+, RCDPeaks was able to cluster a one-million frames trajectory using less than 4.5 GB of RAM, a task that would have taken more than 2 TB and about 3\u00d7 more time with the fastest and less memory-hunger alternative currently available. Other key features of RCDPeaks include the automatic selection of parameters, the screening of center candidates and the geometrical refining of returned clusters.<\/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 RCDPeaks are free and publicly available on GitHub (https:\/\/github.com\/LQCT\/RCDPeaks.git).<\/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\/btac021","type":"journal-article","created":{"date-parts":[[2022,1,7]],"date-time":"2022-01-07T12:18:36Z","timestamp":1641557916000},"page":"1863-1869","source":"Crossref","is-referenced-by-count":7,"title":["RCDPeaks: memory-efficient density peaks clustering of long molecular dynamics"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6454-4320","authenticated-orcid":false,"given":"Daniel","family":"Platero-Rochart","sequence":"first","affiliation":[{"name":"Departamento de Qu\u00edmica-F\u00edsica, Laboratorio de Qu\u00edmica Computacional y Te\u00f3rica (LQCT), Facultad de Qu\u00edmica, Universidad de La Habana , La Habana 10400, Cuba"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3852-4902","authenticated-orcid":false,"given":"Roy","family":"Gonz\u00e1lez-Alem\u00e1n","sequence":"additional","affiliation":[{"name":"Departamento de Qu\u00edmica-F\u00edsica, 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"}]},{"given":"Erix W","family":"Hern\u00e1ndez-Rodr\u00edguez","sequence":"additional","affiliation":[{"name":"Laboratorio de Bioinform\u00e1tica y Qu\u00edmica Computacional (LBQC), Facultad de Medicina, Universidad Cat\u00f3lica del Maule , Talca 3460000, Chile"},{"name":"Escuela de Qu\u00edmica y Farmacia, Facultad de Medicina, Universidad Cat\u00f3lica del Maule , Talca 3460000, 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"}]},{"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 3460000, Chile"}]},{"given":"Luis","family":"Montero-Cabrera","sequence":"additional","affiliation":[{"name":"Departamento de Qu\u00edmica-F\u00edsica, 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":[[2022,1,10]]},"reference":[{"key":"2023020108592996500_btac021-B1","doi-asserted-by":"crossref","first-page":"135","DOI":"10.1016\/j.knosys.2016.02.001","article-title":"Study on density peaks clustering based on k-nearest neighbors and principal component analysis","volume":"99","author":"Du","year":"2016","journal-title":"Knowledge Based Syst"},{"key":"2023020108592996500_btac021-B2","doi-asserted-by":"crossref","first-page":"106350","DOI":"10.1016\/j.knosys.2020.106350","article-title":"Density peaks clustering with gap-based automatic center detection","volume":"206","author":"Flores","year":"2020","journal-title":"Knowledge Based Syst"},{"key":"2023020108592996500_btac021-B3","doi-asserted-by":"crossref","first-page":"444","DOI":"10.1021\/acs.jcim.9b00828","article-title":"BitClust: fast geometrical clustering of long molecular dynamics simulations","volume":"60","author":"Gonz\u00e1lez-Alem\u00e1n","year":"2020","journal-title":"J. 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