{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,2]],"date-time":"2026-04-02T20:11:45Z","timestamp":1775160705437,"version":"3.50.1"},"reference-count":13,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2020,12,12]],"date-time":"2020-12-12T00:00:00Z","timestamp":1607731200000},"content-version":"vor","delay-in-days":1,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["R21AI137580"],"award-info":[{"award-number":["R21AI137580"]}],"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>VIrus Particle ExploreR data base (VIPERdb) (http:\/\/viperdb.scripps.edu) is a curated repository of virus capsid structures and a database of structure-derived data along with various virus specific information. VIPERdb has been continuously improved for over 20 years and contains a number of virus structure analysis tools. The release of VIPERdb v3.0 contains new structure-based data analytics tools like Multiple Structure-based and Sequence Alignment (MSSA) to identify hot-spot residues within a selected group of structures and an anomaly detection application to analyze and curate the structure-derived data within individual virus families. At the time of this writing, there are 931 virus structures from 62 different virus families in the database. Significantly, the new release also contains a standalone database called \u2018Virus World database\u2019 (VWdb) that comprises all the characterized viruses (\u223c181 000) known to date, gathered from ICTVdb and NCBI, and their capsid protein sequences, organized according to their virus taxonomy with links to known structures in VIPERdb and PDB. Moreover, the new release of VIPERdb includes a service-oriented data engine to handle all the data access requests and provides an interface for futuristic data analytics using machine leaning applications.<\/jats:p>","DOI":"10.1093\/nar\/gkaa1096","type":"journal-article","created":{"date-parts":[[2020,12,10]],"date-time":"2020-12-10T21:42:10Z","timestamp":1607636530000},"page":"D809-D816","source":"Crossref","is-referenced-by-count":73,"title":["VIPERdb v3.0: a structure-based data analytics platform for viral capsids"],"prefix":"10.1093","volume":"49","author":[{"given":"Daniel","family":"Montiel-Garcia","sequence":"first","affiliation":[{"name":"Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA"},{"name":"Departments of Computer Systems and Information Technologies, Tecnologico Nacional de Mexico & Instituto Tecnol\u00f3gico Superior de Irapuato, Irapuato, Guanajuato, M\u00e9xico"}]},{"given":"Nelly","family":"Santoyo-Rivera","sequence":"additional","affiliation":[{"name":"Departments of Computer Systems and Information Technologies, Tecnologico Nacional de Mexico & Instituto Tecnol\u00f3gico Superior de Irapuato, Irapuato, Guanajuato, M\u00e9xico"}]},{"given":"Phuong","family":"Ho","sequence":"additional","affiliation":[{"name":"Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA"}]},{"given":"Mauricio","family":"Carrillo-Tripp","sequence":"additional","affiliation":[{"name":"Biomolecular Diversity Laboratory, Centro de Investigaci\u00f3n y de Estudios Avanzados Unidad Monterrey, V\u00eda del Conocimiento 201, Parque PIIT, C.P. 66600, Apodaca, Nuevo Le\u00f3n, M\u00e9xico"}]},{"given":"Charles\u00a0L Brooks","family":"III","sequence":"additional","affiliation":[{"name":"Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA"},{"name":"Department of Chemistry, University of Michigan, Ann Arbor, MI, USA"},{"name":"Department of Biophysics, University of Michigan, Ann Arbor, MI, USA"}]},{"given":"John E","family":"Johnson","sequence":"additional","affiliation":[{"name":"Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4638-8277","authenticated-orcid":false,"given":"Vijay S","family":"Reddy","sequence":"additional","affiliation":[{"name":"Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA"}]}],"member":"286","published-online":{"date-parts":[[2020,12,11]]},"reference":[{"key":"2021010313140221800_B1","doi-asserted-by":"crossref","first-page":"11943","DOI":"10.1128\/JVI.75.24.11943-11947.2001","article-title":"Virus Particle Explorer (VIPER), a website for virus capsid structures and their computational analyses","volume":"75","author":"Reddy","year":"2001","journal-title":"J. Virol."},{"key":"2021010313140221800_B2","doi-asserted-by":"crossref","first-page":"D386","DOI":"10.1093\/nar\/gkj032","article-title":"VIPERdb: a relational database for structural virology","volume":"34","author":"Shepherd","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"2021010313140221800_B3","doi-asserted-by":"crossref","first-page":"D436","DOI":"10.1093\/nar\/gkn840","article-title":"VIPERdb2: an enhanced and web API enabled relational database for structural virology","volume":"37","author":"Carrillo-Tripp","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"2021010313140221800_B4","doi-asserted-by":"crossref","first-page":"477","DOI":"10.1146\/annurev-virology-092917-043405","article-title":"VIPERdb: a tool for virus research","volume":"5","author":"Ho","year":"2018","journal-title":"Annu. Rev. Virol."},{"key":"2021010313140221800_B5","doi-asserted-by":"crossref","first-page":"1441","DOI":"10.1007\/s00705-016-3215-y","article-title":"50 years of the International Committee on Taxonomy of Viruses: progress and prospects","volume":"162","author":"Adams","year":"2017","journal-title":"Arch. Virol."},{"key":"2021010313140221800_B6","doi-asserted-by":"crossref","first-page":"8","DOI":"10.3201\/eid1001.030279","article-title":"Emerging issues in virus taxonomy","volume":"10","author":"van\u00a0Regenmortel","year":"2004","journal-title":"Emerg. Infect. Dis."},{"key":"2021010313140221800_B7","doi-asserted-by":"crossref","first-page":"D7","DOI":"10.1093\/nar\/gkv1290","article-title":"Database resources of the National Center for Biotechnology Information","volume":"44","author":"Coordinators","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"2021010313140221800_B8","doi-asserted-by":"crossref","first-page":"D12","DOI":"10.1093\/nar\/gkw1071","article-title":"Database resources of the National Center for Biotechnology Information","volume":"45","author":"Coordinators","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"2021010313140221800_B9","first-page":"243","volume-title":"Proc. of the Annual IEEE Visualization Conference","author":"Bajaj","year":"2004"},{"key":"2021010313140221800_B10","doi-asserted-by":"crossref","first-page":"1605","DOI":"10.1002\/jcc.20084","article-title":"UCSF Chimera\u2013a visualization system for exploratory research and analysis","volume":"25","author":"Pettersen","year":"2004","journal-title":"J. Comput. Chem."},{"key":"2021010313140221800_B11","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1093\/nar\/28.1.235","article-title":"The protein data bank","volume":"28","author":"Berman","year":"2000","journal-title":"Nucleic Acids Res."},{"key":"2021010313140221800_B12","doi-asserted-by":"crossref","first-page":"D506","DOI":"10.1093\/nar\/gky1049","article-title":"UniProt: a worldwide hub of protein knowledge","volume":"47","author":"UniProt","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2021010313140221800_B13","doi-asserted-by":"crossref","first-page":"2650","DOI":"10.1093\/bioinformatics\/btw300","article-title":"Calculating and scoring high quality multiple flexible protein structure alignments","volume":"32","author":"Ritchie","year":"2016","journal-title":"Bioinformatics"}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/nar\/article-pdf\/49\/D1\/D809\/35364004\/gkaa1096.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"http:\/\/academic.oup.com\/nar\/article-pdf\/49\/D1\/D809\/35364004\/gkaa1096.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,1,3]],"date-time":"2021-01-03T18:20:21Z","timestamp":1609698021000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/article\/49\/D1\/D809\/6031427"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,12,11]]},"references-count":13,"journal-issue":{"issue":"D1","published-online":{"date-parts":[[2020,12,11]]},"published-print":{"date-parts":[[2021,1,8]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gkaa1096","relation":{},"ISSN":["0305-1048","1362-4962"],"issn-type":[{"value":"0305-1048","type":"print"},{"value":"1362-4962","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2021,1,8]]},"published":{"date-parts":[[2020,12,11]]}}}