{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,29]],"date-time":"2026-04-29T19:57:05Z","timestamp":1777492625351,"version":"3.51.4"},"reference-count":37,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2021,11,11]],"date-time":"2021-11-11T00:00:00Z","timestamp":1636588800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100014440","name":"Ministry of Science, Innovation and Universities","doi-asserted-by":"publisher","award":["FPU16\/01209"],"award-info":[{"award-number":["FPU16\/01209"]}],"id":[{"id":"10.13039\/100014440","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002809","name":"Government of Catalonia","doi-asserted-by":"publisher","award":["DGRIS"],"award-info":[{"award-number":["DGRIS"]}],"id":[{"id":"10.13039\/501100002809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"EU H2020","award":["101003551"],"award-info":[{"award-number":["101003551"]}]},{"name":"CINECA","award":["GSNSDr3"],"award-info":[{"award-number":["GSNSDr3"]}]},{"name":"CINECA","award":["GSNSDr2"],"award-info":[{"award-number":["GSNSDr2"]}]},{"DOI":"10.13039\/501100001711","name":"Swiss National Science Foundation","doi-asserted-by":"publisher","award":["192780"],"award-info":[{"award-number":["192780"]}],"id":[{"id":"10.13039\/501100001711","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,1,7]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>SCoV2-MD (www.scov2-md.org) is a new online resource that systematically organizes atomistic simulations of the SARS-CoV-2 proteome. The database includes simulations produced by leading groups using molecular dynamics (MD) methods to investigate the structure-dynamics-function relationships of viral proteins. SCoV2-MD cross-references the molecular data with the pandemic evolution by tracking all available variants sequenced during the pandemic and deposited in the GISAID resource. SCoV2-MD enables the interactive analysis of the deposited trajectories through a web interface, which enables users to search by viral protein, isolate, phylogenetic attributes, or specific point mutation. Each mutation can then be analyzed interactively combining static (e.g. a variety of amino acid substitution penalties) and dynamic (time-dependent data derived from the dynamics of the local geometry) scores. Dynamic scores can be computed on the basis of nine non-covalent interaction types, including steric properties, solvent accessibility, hydrogen bonding, and other types of chemical interactions. Where available, experimental data such as antibody escape and change in binding affinities from deep mutational scanning experiments are also made available. All metrics can be combined to build predefined or custom scores to interrogate the impact of evolving variants on protein structure and function.<\/jats:p>","DOI":"10.1093\/nar\/gkab977","type":"journal-article","created":{"date-parts":[[2021,11,8]],"date-time":"2021-11-08T20:14:06Z","timestamp":1636402446000},"page":"D858-D866","source":"Crossref","is-referenced-by-count":28,"title":["SCoV2-MD: a database for the dynamics of the SARS-CoV-2 proteome and variant impact predictions"],"prefix":"10.1093","volume":"50","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6233-8945","authenticated-orcid":false,"given":"Mariona","family":"Torrens-Fontanals","sequence":"first","affiliation":[{"name":"Research Programme on Biomedical Informatics, Hospital del Mar Medical Research Institute\u2014Department of Experimental and Health Sciences, Pompeu Fabra University, Barcelona\u00a008003, Spain"}]},{"given":"Alejandro","family":"Peralta-Garc\u00eda","sequence":"additional","affiliation":[{"name":"Research Programme on Biomedical Informatics, Hospital del Mar Medical Research Institute\u2014Department of Experimental and Health Sciences, Pompeu Fabra University, Barcelona\u00a008003, Spain"}]},{"given":"Carmine","family":"Talarico","sequence":"additional","affiliation":[{"name":"EXSCALATE, Domp\u00e9 Farmaceutici S.p.A., Via Tommaso De Amicis, 95, Napoli, 80131, Italy"}]},{"given":"Ramon","family":"Guix\u00e0-Gonz\u00e1lez","sequence":"additional","affiliation":[{"name":"Laboratory of Biomolecular Research, Paul Scherrer Institute, CH-5232 Villigen PSI, Switzerland"},{"name":"Condensed Matter Theory Group, Paul Scherrer Institute, CH-5232 Villigen PSI, Switzerland"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6449-0596","authenticated-orcid":false,"given":"Toni","family":"Giorgino","sequence":"additional","affiliation":[{"name":"Biophysics Institute (CNR-IBF), National Research Council of Italy, Milan\u00a020133, Italy"},{"name":"Department of Biosciences, University of Milan, Milan\u00a020133, Italy"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1844-4449","authenticated-orcid":false,"given":"Jana","family":"Selent","sequence":"additional","affiliation":[{"name":"Research Programme on Biomedical Informatics, Hospital del Mar Medical Research Institute\u2014Department of Experimental and Health Sciences, Pompeu Fabra University, Barcelona\u00a008003, Spain"}]}],"member":"286","published-online":{"date-parts":[[2021,11,11]]},"reference":[{"key":"2022040807124678200_B1","doi-asserted-by":"crossref","first-page":"409","DOI":"10.1038\/s41579-021-00573-0","article-title":"SARS-CoV-2 variants, spike mutations and immune escape","volume":"19","author":"Harvey","year":"2021","journal-title":"Nat. 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