{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,22]],"date-time":"2025-02-22T00:44:56Z","timestamp":1740185096226,"version":"3.37.3"},"reference-count":8,"publisher":"Oxford University Press (OUP)","issue":"13","license":[{"start":{"date-parts":[[2017,2,17]],"date-time":"2017-02-17T00:00:00Z","timestamp":1487289600000},"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":["R33-GM078601","R01-GM100701"],"award-info":[{"award-number":["R33-GM078601","R01-GM100701"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["NSF DBI-0829586","NSF DBI DBI-1338415"],"award-info":[{"award-number":["NSF DBI-0829586","NSF DBI DBI-1338415"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>We developed a new software tool, BioJava-ModFinder, for identifying protein modifications observed in 3D structures archived in the Protein Data Bank (PDB). Information on more than 400 types of protein modifications were collected and curated from annotations in PDB, RESID, and PSI-MOD. We divided these modifications into three categories: modified residues, attachment modifications, and cross-links. We have developed a systematic method to identify these modifications in 3D protein structures. We have integrated this package with the RCSB PDB web application and added protein modification annotations to the sequence diagram and structure display. By scanning all 3D structures in the PDB using BioJava-ModFinder, we identified more than 30\u00a0000 structures with protein modifications, which can be searched, browsed, and visualized on the RCSB PDB website.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and Implementation<\/jats:title>\n                  <jats:p>BioJava-ModFinder is available as open source (LGPL license) at (https:\/\/github.com\/biojava\/biojava\/tree\/master\/biojava-modfinder). The RCSB PDB can be accessed at http:\/\/www.rcsb.org.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btx101","type":"journal-article","created":{"date-parts":[[2017,2,16]],"date-time":"2017-02-16T21:28:08Z","timestamp":1487280488000},"page":"2047-2049","source":"Crossref","is-referenced-by-count":8,"title":["BioJava-ModFinder: identification of protein modifications in 3D structures from the Protein Data Bank"],"prefix":"10.1093","volume":"33","author":[{"given":"Jianjiong","family":"Gao","sequence":"first","affiliation":[{"name":"Department of Computer Science and C.S. Bond Life Sciences Center, University of Missouri, Columbia, MO, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Andreas","family":"Prli\u0107","sequence":"additional","affiliation":[{"name":"RCSB Protein Data Bank, San Diego Supercomputer Center, University of California San Diego, La Jolla, CA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chunxiao","family":"Bi","sequence":"additional","affiliation":[{"name":"RCSB Protein Data Bank, San Diego Supercomputer Center, University of California San Diego, La Jolla, CA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wolfgang F","family":"Bluhm","sequence":"additional","affiliation":[{"name":"RCSB Protein Data Bank, San Diego Supercomputer Center, University of California San Diego, La Jolla, CA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dimitris","family":"Dimitropoulos","sequence":"additional","affiliation":[{"name":"RCSB Protein Data Bank, San Diego Supercomputer Center, University of California San Diego, La Jolla, CA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dong","family":"Xu","sequence":"additional","affiliation":[{"name":"Department of Computer Science and C.S. Bond Life Sciences Center, University of Missouri, Columbia, MO, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Philip E","family":"Bourne","sequence":"additional","affiliation":[{"name":"RCSB Protein Data Bank, San Diego Supercomputer Center, University of California San Diego, La Jolla, CA, USA"},{"name":"Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Peter W","family":"Rose","sequence":"additional","affiliation":[{"name":"RCSB Protein Data Bank, San Diego Supercomputer Center, University of California San Diego, La Jolla, CA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2017,2,17]]},"reference":[{"key":"2023020206014273400_btx101-B1","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":"2023020206014273400_btx101-B2","doi-asserted-by":"crossref","first-page":"5603","DOI":"10.1074\/jbc.M108916200","article-title":"Azotobacter vinelandii ferredoxin I: a sequence and structure comparison approach to alteration of [4Fe-4S]2+\/+ reduction potential","volume":"277","author":"Chen","year":"2002","journal-title":"J. Biol. Chem"},{"key":"2023020206014273400_btx101-B4","doi-asserted-by":"crossref","first-page":"1537","DOI":"10.1002\/pmic.200300764","article-title":"Annotation of post-translational modifications in the Swiss-Prot knowledge base","volume":"4","author":"Farriol-Mathis","year":"2004","journal-title":"Proteomics"},{"key":"2023020206014273400_btx101-B5","doi-asserted-by":"crossref","first-page":"1527","DOI":"10.1002\/pmic.200300777","article-title":"The RESID Database of protein modifications as a resource and annotation tool","volume":"4","author":"Garavelli","year":"2004","journal-title":"Proteomics"},{"key":"2023020206014273400_btx101-B6","doi-asserted-by":"crossref","first-page":"864","DOI":"10.1038\/nbt0808-864","article-title":"The PSI-MOD community standard for representation of protein modification data","volume":"26","author":"Montecchi-Palazzi","year":"2008","journal-title":"Nat. Biotechnol"},{"key":"2023020206014273400_btx101-B7","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":"2023020206014273400_btx101-B8","doi-asserted-by":"crossref","first-page":"D392","DOI":"10.1093\/nar\/gkq1021","article-title":"The RCSB Protein Data Bank: redesigned web site and web services","volume":"39","author":"Rose","year":"2011","journal-title":"Nucleic Acids Res"},{"key":"2023020206014273400_btx101-B9","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":"2015","journal-title":"Nucleic Acids Res"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/13\/2047\/49040465\/bioinformatics_33_13_2047.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/13\/2047\/49040465\/bioinformatics_33_13_2047.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T06:02:40Z","timestamp":1675317760000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/33\/13\/2047\/3002764"}},"subtitle":[],"editor":[{"given":"Alfonso","family":"Valencia","sequence":"additional","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2017,2,17]]},"references-count":8,"journal-issue":{"issue":"13","published-print":{"date-parts":[[2017,7,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btx101","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"type":"print","value":"1367-4803"},{"type":"electronic","value":"1367-4811"}],"subject":[],"published-other":{"date-parts":[[2017,7,1]]},"published":{"date-parts":[[2017,2,17]]}}}