{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,5]],"date-time":"2026-02-05T20:18:54Z","timestamp":1770322734997,"version":"3.49.0"},"reference-count":14,"publisher":"Oxford University Press (OUP)","issue":"24","license":[{"start":{"date-parts":[[2016,11,16]],"date-time":"2016-11-16T00:00:00Z","timestamp":1479254400000},"content-version":"vor","delay-in-days":86,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"NSF","award":["DBI-1338415"],"award-info":[{"award-number":["DBI-1338415"]}]},{"name":"Department of Energy and the National Institutes of Health"},{"name":"The State University of New Jersey and the University of California at San Diego"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,12,15]]},"abstract":"<jats:p>Summary: The Protein Data Bank (PDB) now contains more than 120,000 three-dimensional (3D) structures of biological macromolecules. To allow an interpretation of how PDB data relates to other publicly available annotations, we developed a novel data integration platform that maps 3D structural information across various datasets. This integration bridges from the human genome across protein sequence to 3D structure space. We developed novel software solutions for data management and visualization, while incorporating new libraries for web-based visualization using SVG graphics.<\/jats:p>\n               <jats:p>Availability and Implementation: The new views are available from http:\/\/www.rcsb.org and software is available from https:\/\/github.com\/rcsb\/.<\/jats:p>\n               <jats:p>Contact: \u00a0andreas.prlic@rcsb.org<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btw547","type":"journal-article","created":{"date-parts":[[2016,8,23]],"date-time":"2016-08-23T00:28:57Z","timestamp":1471912137000},"page":"3833-3835","source":"Crossref","is-referenced-by-count":16,"title":["Integrating genomic information with protein sequence and 3D atomic level structure at the RCSB protein data bank"],"prefix":"10.1093","volume":"32","author":[{"given":"Andreas","family":"Prli\u0107","sequence":"first","affiliation":[{"name":"1RCSB Protein Data Bank, University of California San Diego, San Diego Supercomputer Center, La Jolla, CA 92093, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tara","family":"Kalro","sequence":"additional","affiliation":[{"name":"1RCSB Protein Data Bank, University of California San Diego, San Diego Supercomputer Center, La Jolla, CA 92093, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Roshni","family":"Bhattacharya","sequence":"additional","affiliation":[{"name":"3Bioinformatics and Medical Informatics, San Diego State University, San Diego, CA 92182, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Cole","family":"Christie","sequence":"additional","affiliation":[{"name":"1RCSB Protein Data Bank, University of California San Diego, San Diego Supercomputer Center, La Jolla, CA 92093, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Stephen K.","family":"Burley","sequence":"additional","affiliation":[{"name":"1RCSB Protein Data Bank, University of California San Diego, San Diego Supercomputer Center, La Jolla, CA 92093, USA"},{"name":"2RCSB Protein Data Bank, Department of Chemistry and Chemical Biology, Center for Integrative Proteomics Research, Institute for Quantitative Biomedicine, and Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Peter W.","family":"Rose","sequence":"additional","affiliation":[{"name":"1RCSB Protein Data Bank, University of California San Diego, San Diego Supercomputer Center, La Jolla, CA 92093, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2016,8,22]]},"reference":[{"key":"2023020114102499100_btw547-B1","doi-asserted-by":"crossref","first-page":"889","DOI":"10.1093\/bioinformatics\/btr020","article-title":"Dalliance: interactive genome viewing on the web","volume":"27","author":"Down","year":"2011","journal-title":"Bioinformatics"},{"key":"2023020114102499100_btw547-B2","first-page":"44, D279\u2013D285","article-title":"The Pfam protein families database: towards a more sustainable future","author":"Finn","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2023020114102499100_btw547-B3","doi-asserted-by":"crossref","first-page":"D1079","DOI":"10.1093\/nar\/gku1071","article-title":"Genenames.org: the HGNC resources in 2015","volume":"43","author":"Gray","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2023020114102499100_btw547-B4","doi-asserted-by":"crossref","first-page":"1250","DOI":"10.1107\/S0021889810030256","article-title":"Jmol\u2014a paradigm shift in crystallographic visualization","volume":"43","author":"Hanson","year":"2010","journal-title":"J. Appl. Crystallogr"},{"key":"2023020114102499100_btw547-B5","doi-asserted-by":"crossref","first-page":"D512","DOI":"10.1093\/nar\/gku1267","article-title":"PhosphoSitePlus, 2014: mutations, PTMs and recalibrations","volume":"43","author":"Hornbeck","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2023020114102499100_btw547-B6","doi-asserted-by":"crossref","first-page":"2693","DOI":"10.1093\/bioinformatics\/bts494","article-title":"BioJava: an open-source framework for bioinformatics in 2012","volume":"28","author":"Prli\u0107","year":"2012","journal-title":"Bioinformatics"},{"key":"2023020114102499100_btw547-B7","doi-asserted-by":"crossref","first-page":"e1002802.","DOI":"10.1371\/journal.pcbi.1002802","article-title":"Ten Simple Rules for the Open Development of Scientific Software","volume":"8","author":"Prli\u0107","year":"2012","journal-title":"PLoS Comput. Biol"},{"key":"2023020114102499100_btw547-B8","doi-asserted-by":"crossref","first-page":"1395","DOI":"10.1016\/j.str.2011.08.006","article-title":"A new generation of crystallographic validation tools for the Protein Data Bank","volume":"19","author":"Read","year":"2011","journal-title":"Structure"},{"key":"2023020114102499100_btw547-B9","doi-asserted-by":"crossref","first-page":"W576","DOI":"10.1093\/nar\/gkv402","article-title":"NGL Viewer: a web application for molecular visualization","volume":"43","author":"Rose","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2023020114102499100_btw547-B10","doi-asserted-by":"crossref","first-page":"D345","DOI":"10.1093\/nar\/gku1214","article-title":"The RCSB Protein Data Bank: views of structural biology for basic and applied research and education","volume":"43","author":"Rose","year":"2014","journal-title":"Nucleic Acids Res"},{"key":"2023020114102499100_btw547-B11","doi-asserted-by":"crossref","first-page":"D670","DOI":"10.1093\/nar\/gku1177","article-title":"The UCSC Genome Browser database: 2015 update","volume":"43","author":"Rosenbloom","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2023020114102499100_btw547-B12","doi-asserted-by":"crossref","first-page":"D204","DOI":"10.1093\/nar\/gku989","article-title":"UniProt: a hub for protein information","volume":"43","author":"The UniProt Consortium","year":"2014","journal-title":"Nucleic Acids Res"},{"key":"2023020114102499100_btw547-B13","doi-asserted-by":"crossref","first-page":"D483","DOI":"10.1093\/nar\/gks1258","article-title":"SIFTS: structure integration with function, taxonomy and sequences resource","volume":"41","author":"Velankar","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"2023020114102499100_btw547-B14","doi-asserted-by":"crossref","first-page":"D710","DOI":"10.1093\/nar\/gkv1157","article-title":"Ensembl 2016","volume":"44","author":"Yates","year":"2016","journal-title":"Nucleic Acids Res"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/32\/24\/3833\/49027000\/bioinformatics_32_24_3833.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/32\/24\/3833\/49027000\/bioinformatics_32_24_3833.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T00:01:24Z","timestamp":1675296084000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/32\/24\/3833\/2525659"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016,8,22]]},"references-count":14,"journal-issue":{"issue":"24","published-print":{"date-parts":[[2016,12,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btw547","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2016,12,15]]},"published":{"date-parts":[[2016,8,22]]}}}