{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,27]],"date-time":"2026-01-27T07:13:10Z","timestamp":1769497990811,"version":"3.49.0"},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"23","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2005,12,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: UniProtKB\/SwissProt is the main resource for detailed annotations of protein sequences. This database provides a jumping-off point to many other resources through the links it provides. Among others, these include other primary databases, secondary databases, the Gene Ontology and OMIM. While a large number of links are provided to Protein Data Bank (PDB) files, obtaining a regularly updated mapping between UniProtKB entries and PDB entries at the chain or residue level is not straightforward. In particular, there is no regularly updated resource which allows a UniProtKB\/SwissProt entry to be identified for a given residue of a PDB file.<\/jats:p>\n               <jats:p>Results: We have created a completely automatically maintained database which maps PDB residues to residues in UniProtKB\/SwissProt and UniProtKB\/trEMBL entries. The protocol uses links from PDB to UniProtKB, from UniProtKB to PDB and a brute-force sequence scan to resolve PDB chains for which no annotated link is available. Finally the sequences from PDB and UniProtKB are aligned to obtain a residue-level mapping.<\/jats:p>\n               <jats:p>Availability: The resource may be queried interactively or downloaded from<\/jats:p>\n               <jats:p>Contact: \u00a0andrew@bioinf.org.uk<\/jats:p>","DOI":"10.1093\/bioinformatics\/bti694","type":"journal-article","created":{"date-parts":[[2005,9,28]],"date-time":"2005-09-28T03:23:31Z","timestamp":1127877811000},"page":"4297-4301","source":"Crossref","is-referenced-by-count":79,"title":["Mapping PDB chains to UniProtKB entries"],"prefix":"10.1093","volume":"21","author":[{"given":"Andrew C. R.","family":"Martin","sequence":"first","affiliation":[]}],"member":"286","published-online":{"date-parts":[[2005,9,27]]},"reference":[{"key":"2023061010032789700_b1","doi-asserted-by":"crossref","first-page":"D154","DOI":"10.1093\/nar\/gki070","article-title":"The Universal Protein Resource (UniProt)","volume":"33","author":"Bairoch","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"2023061010032789700_b2","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":"2023061010032789700_b3","doi-asserted-by":"crossref","first-page":"365","DOI":"10.1093\/nar\/gkg095","article-title":"The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003","volume":"31","author":"Boeckmann","year":"2003","journal-title":"Nuclec Acids Res."},{"key":"2023061010032789700_b4","doi-asserted-by":"crossref","first-page":"1443","DOI":"10.1093\/bioinformatics\/bti220","article-title":"Mapping SNPs to protein sequence and structure data","volume":"21","author":"Cavallo","year":"2005","journal-title":"Bioinformatics"},{"key":"2023061010032789700_b5","doi-asserted-by":"crossref","first-page":"6247","DOI":"10.1046\/j.0014-2956.2001.02581.x","article-title":"Solution structure of the mEGF\/TGFalpha44-50 chimeric growth factor","volume":"268","author":"Chamberlin","year":"2001","journal-title":"Eur. 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USA"},{"key":"2023061010032789700_b11","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1038\/43487","article-title":"Structure of Tetrahymena GCN5 bound to coenzyme A and a histone H3 peptide","volume":"401","author":"Rojas","year":"1999","journal-title":"Nature (London)"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/21\/23\/4297\/50567315\/bioinformatics_21_23_4297.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/21\/23\/4297\/50567315\/bioinformatics_21_23_4297.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,6,10]],"date-time":"2023-06-10T10:03:55Z","timestamp":1686391435000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/21\/23\/4297\/194996"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2005,9,27]]},"references-count":11,"journal-issue":{"issue":"23","published-print":{"date-parts":[[2005,12,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bti694","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2005,12]]},"published":{"date-parts":[[2005,9,27]]}}}