{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:41:20Z","timestamp":1772138480754,"version":"3.50.1"},"reference-count":26,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2020,9,5]],"date-time":"2020-09-05T00:00:00Z","timestamp":1599264000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["GM126299"],"award-info":[{"award-number":["GM126299"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,1,8]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>SARS-CoV-2, the etiologic agent of COVID-19, exemplifies the general threat to global health posed by coronaviruses. The urgent need for effective vaccines and therapies is leading to a rapid rise in the number of high resolution structures of SARS-CoV-2 proteins that collectively reveal a map of virus vulnerabilities. To assist structure-based design of vaccines and therapeutics against SARS-CoV-2 and other coronaviruses, we have developed CoV3D, a database and resource for coronavirus protein structures, which is updated on a weekly basis. CoV3D provides users with comprehensive sets of structures of coronavirus proteins and their complexes with antibodies, receptors, and small molecules. Integrated molecular viewers allow users to visualize structures of the spike glycoprotein, which is the major target of neutralizing antibodies and vaccine design efforts, as well as sets of spike-antibody complexes, spike sequence variability, and known polymorphisms. In order to aid structure-based design and analysis of the spike glycoprotein, CoV3D permits visualization and download of spike structures with modeled N-glycosylation at known glycan sites, and contains structure-based classification of spike conformations, generated by unsupervised clustering. CoV3D can serve the research community as a centralized reference and resource for spike and other coronavirus protein structures, and is available at: https:\/\/cov3d.ibbr.umd.edu.<\/jats:p>","DOI":"10.1093\/nar\/gkaa731","type":"journal-article","created":{"date-parts":[[2020,8,22]],"date-time":"2020-08-22T07:12:18Z","timestamp":1598080338000},"page":"D282-D287","source":"Crossref","is-referenced-by-count":72,"title":["CoV3D: a database of high resolution coronavirus protein structures"],"prefix":"10.1093","volume":"49","author":[{"given":"Ragul","family":"Gowthaman","sequence":"first","affiliation":[{"name":"University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA"},{"name":"Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA"}]},{"given":"Johnathan D","family":"Guest","sequence":"additional","affiliation":[{"name":"University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA"},{"name":"Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA"}]},{"given":"Rui","family":"Yin","sequence":"additional","affiliation":[{"name":"University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA"},{"name":"Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA"}]},{"given":"Jared","family":"Adolf-Bryfogle","sequence":"additional","affiliation":[{"name":"Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA"},{"name":"IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA"},{"name":"Institute for Protein Innovation, Boston, MA 02115, USA"},{"name":"Division of Hematology\/Oncology, Boston Children's Hospital, Boston, MA 02115, USA"},{"name":"Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA"}]},{"given":"William R","family":"Schief","sequence":"additional","affiliation":[{"name":"Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA"},{"name":"IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA"},{"name":"The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA 02139, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4821-0368","authenticated-orcid":false,"given":"Brian G","family":"Pierce","sequence":"additional","affiliation":[{"name":"University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA"},{"name":"Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA"}]}],"member":"286","published-online":{"date-parts":[[2020,9,5]]},"reference":[{"key":"2021010313110730000_B1","doi-asserted-by":"crossref","first-page":"523","DOI":"10.1038\/nrmicro.2016.81","article-title":"SARS and MERS: recent insights into emerging coronaviruses","volume":"14","author":"de\u00a0Wit","year":"2016","journal-title":"Nat. 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