{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,21]],"date-time":"2026-10-21T04:03:27Z","timestamp":1792555407691,"version":"4.5.0"},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"18","license":[{"start":{"date-parts":[[2019,2,13]],"date-time":"2019-02-13T00:00:00Z","timestamp":1550016000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100013060","name":"European Molecular Biology Laboratory","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100013060","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100013060","name":"EMBL","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100013060","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010269","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["104948"],"award-info":[{"award-number":["104948"]}],"id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,9,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Cofactors are essential for many enzyme reactions. The Protein Data Bank (PDB) contains &amp;gt;67\u2009000 entries containing enzyme structures, many with bound cofactor or cofactor-like molecules. This work aims to identify and categorize these small molecules in the PDB and make it easier to find them.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>The Protein Data Bank in Europe (PDBe; pdbe.org) has implemented a pipeline to identify enzyme cofactor and cofactor-like molecules, which are now part of the PDBe weekly release process.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Information is made available on the individual PDBe entry pages at pdbe.org and programmatically through the PDBe REST API (pdbe.org\/api).<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btz115","type":"journal-article","created":{"date-parts":[[2019,2,13]],"date-time":"2019-02-13T21:17:48Z","timestamp":1550092668000},"page":"3510-3511","source":"Crossref","is-referenced-by-count":34,"title":["Finding enzyme cofactors in Protein Data Bank"],"prefix":"10.1093","volume":"35","author":[{"given":"Abhik","family":"Mukhopadhyay","sequence":"first","affiliation":[{"name":"European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute (EMBL-EBI) , Cambridge, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Neera","family":"Borkakoti","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute (EMBL-EBI) , Cambridge, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Luk\u00e1\u0161","family":"Pravda","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute (EMBL-EBI) , Cambridge, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jonathan D","family":"Tyzack","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute (EMBL-EBI) , Cambridge, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Janet M","family":"Thornton","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute (EMBL-EBI) , Cambridge, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sameer","family":"Velankar","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute (EMBL-EBI) , Cambridge, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2019,2,13]]},"reference":[{"key":"2023013108061000200_btz115-B1","doi-asserted-by":"crossref","first-page":"D482","DOI":"10.1093\/nar\/gky1114","article-title":"SIFTS: updated structure integration with function, taxonomy and sequences resource allows 40-fold increase in coverage of structure-based annotations for proteins","volume":"47","author":"Dana","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2023013108061000200_btz115-B2","doi-asserted-by":"crossref","first-page":"2496","DOI":"10.1093\/bioinformatics\/btq442","article-title":"The cofactor database: organic cofactors in enzyme catalysis","volume":"26","author":"Fischer","year":"2010","journal-title":"Bioinformatics"},{"key":"2023013108061000200_btz115-B3","doi-asserted-by":"crossref","first-page":"D486","DOI":"10.1093\/nar\/gkx1070","article-title":"PDBe: towards reusable data delivery infrastructure at protein data bank in europe","volume":"46","author":"Mir","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"2023013108061000200_btz115-B4","doi-asserted-by":"crossref","first-page":"D380","DOI":"10.1093\/nar\/gkw952","article-title":"BRENDA in 2017: new perspectives and new tools in BRENDA","volume":"45","author":"Placzek","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"2023013108061000200_btz115-B5","doi-asserted-by":"crossref","first-page":"343","DOI":"10.1021\/ci200444d","article-title":"SiteBinder: an improved approach for comparing multiple protein structural motifs","volume":"52","author":"Sehnal","year":"2012","journal-title":"J. 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