{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,17]],"date-time":"2026-01-17T22:15:27Z","timestamp":1768688127312,"version":"3.49.0"},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"14","license":[{"start":{"date-parts":[[2018,3,2]],"date-time":"2018-03-02T00:00:00Z","timestamp":1519948800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01-GM100701"],"award-info":[{"award-number":["R01-GM100701"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Danish Council for Independent Research\u2013Technology and Production Sciences","award":["DFF|FTP 4005-00082"],"award-info":[{"award-number":["DFF|FTP 4005-00082"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,7,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Oxidative stress and protein damage have been associated with over 200 human ailments including cancer, stroke, neuro-degenerative diseases and aging. Protein carbonylation, a chemically diverse oxidative post-translational modification, is widely considered as the biomarker for oxidative stress and protein damage. Despite their importance and extensive studies, no database\/resource on carbonylated proteins\/sites exists. As such information is very useful to research in biology\/medicine, we have manually curated a data-resource (CarbonylDB) of experimentally-confirmed carbonylated proteins\/sites.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>The CarbonylDB currently contains 1495 carbonylated proteins and 3781 sites from 21 species, with human, rat and yeast as the top three species. We have made further analyses of these carbonylated proteins\/sites and presented their occurrence and occupancy patterns. Carbonylation site data on serum albumin, in particular, provides a fine model system to understand the dynamics of oxidative protein modifications\/damage.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The CarbonylDB is available as a web-resource and for download at http:\/\/digbio.missouri.edu\/CarbonylDB\/.<\/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\/bty123","type":"journal-article","created":{"date-parts":[[2018,3,1]],"date-time":"2018-03-01T13:30:56Z","timestamp":1519911056000},"page":"2518-2520","source":"Crossref","is-referenced-by-count":21,"title":["CarbonylDB: a curated data-resource of protein carbonylation sites"],"prefix":"10.1093","volume":"34","author":[{"given":"R Shyama Prasad","family":"Rao","sequence":"first","affiliation":[{"name":"Biostatistics and Bioinformatics Division, Yenepoya Research Center, Yenepoya University, Mangalore, Karnataka, India"}]},{"given":"Ning","family":"Zhang","sequence":"additional","affiliation":[{"name":"Informatics Institute, University of Missouri-Columbia, MO, USA"},{"name":"C.S. Bond Life Sciences Center, University of Missouri-Columbia, MO, USA"}]},{"given":"Dong","family":"Xu","sequence":"additional","affiliation":[{"name":"Informatics Institute, University of Missouri-Columbia, MO, USA"},{"name":"C.S. Bond Life Sciences Center, University of Missouri-Columbia, MO, USA"},{"name":"Department of Electrical Engineering and Computer Science, University of Missouri-Columbia,Columbia, MO, USA"}]},{"given":"Ian Max","family":"M\u00f8ller","sequence":"additional","affiliation":[{"name":"Department of Molecular Biology and Genetics, Aarhus University, Slagelse, Denmark"}]}],"member":"286","published-online":{"date-parts":[[2018,3,2]]},"reference":[{"key":"2023012713020104700_bty123-B1","doi-asserted-by":"crossref","first-page":"329","DOI":"10.1016\/j.str.2015.11.006","article-title":"Highly charged proteins: the Achilles\u2019 heel of aging proteomes","volume":"24","author":"de Graff","year":"2016","journal-title":"Structure"},{"key":"2023012713020104700_bty123-B2","doi-asserted-by":"crossref","first-page":"79","DOI":"10.1002\/mas.21381","article-title":"Protein carbonylation as a major hallmark of oxidative damage: update of analytical strategies","volume":"33","author":"Fedorova","year":"2014","journal-title":"Mass Spectrom. Rev"},{"key":"2023012713020104700_bty123-B3","doi-asserted-by":"crossref","first-page":"40","DOI":"10.1016\/j.jprot.2016.12.019","article-title":"A biotin enrichment strategy identifies novel carbonylated amino acids in proteins from human plasma","volume":"156","author":"Havelund","year":"2017","journal-title":"J. Proteomics"},{"key":"2023012713020104700_bty123-B4","doi-asserted-by":"crossref","first-page":"1217","DOI":"10.1074\/mcp.M114.043729","article-title":"Protein methionine sulfoxide dynamics in Arabidopsis thaliana under oxidative stress","volume":"14","author":"Jacques","year":"2015","journal-title":"Mol. 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Proteomics"},{"key":"2023012713020104700_bty123-B7","doi-asserted-by":"crossref","first-page":"4166","DOI":"10.1002\/pmic.201100223","article-title":"Pattern of occurrence and occupancy of carbonylation sites in proteins","volume":"11","author":"Rao","year":"2011","journal-title":"Proteomics"},{"key":"2023012713020104700_bty123-B8","doi-asserted-by":"crossref","first-page":"416","DOI":"10.1002\/9781119374947","volume-title":"Protein Carbonylation: Principles, Analysis, and Biological Implications","author":"Ros","year":"2017"},{"key":"2023012713020104700_bty123-B9","doi-asserted-by":"crossref","first-page":"2551","DOI":"10.1093\/bioinformatics\/bts468","article-title":"RedoxDB\u2013a curated database for experimentally verified protein oxidative modification","volume":"28","author":"Sun","year":"2012","journal-title":"Bioinformatics"},{"key":"2023012713020104700_bty123-B10","doi-asserted-by":"crossref","first-page":"66.","DOI":"10.1186\/s12859-017-1472-8","article-title":"Investigation and identification of protein carbonylation sites based on position-specific amino acid composition and physicochemical features","volume":"18","author":"Weng","year":"2017","journal-title":"BMC Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/14\/2518\/48918250\/bioinformatics_34_14_2518.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/14\/2518\/48918250\/bioinformatics_34_14_2518.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,27]],"date-time":"2023-01-27T13:53:30Z","timestamp":1674827610000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/34\/14\/2518\/4917354"}},"subtitle":[],"editor":[{"given":"Jonathan","family":"Wren","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2018,3,2]]},"references-count":10,"journal-issue":{"issue":"14","published-print":{"date-parts":[[2018,7,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bty123","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2018,7,15]]},"published":{"date-parts":[[2018,3,2]]}}}