{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,12]],"date-time":"2026-05-12T20:06:47Z","timestamp":1778616407802,"version":"3.51.4"},"reference-count":16,"publisher":"Oxford University Press (OUP)","issue":"19","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,10,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Redox regulation and signaling, which are involved in various cellular processes, have become one of the research focuses in the past decade. Cysteine thiol groups are particularly susceptible to post-translational modification, and their reversible oxidation is of critical role in redox regulation and signaling. With the tremendous improvement of techniques, hundreds of redox proteins along with their redox-sensitive cysteines have been reported, and the number is still fast growing. However, until now there is no database to accommodate the rapid accumulation of information on protein oxidative modification. Here we present RedoxDB\u2014a manually curated database for experimentally validated redox proteins. RedoxDB (version 1.0) consists of two datasets (A and B, for proteins with or without verified modified cysteines, respectively) and includes 2157 redox proteins containing 2203 cysteine residues with oxidative modification. For each modified cysteine, the exact position, modification type and flanking sequence are provided. Additional information, including gene name, organism, sequence, literature references and links to UniProt and PDB, is also supplied. The database supports several functions including data search, blast and browsing. Bulk download of the entire dataset is also available. We expect that RedoxDB will be useful for both experimental studies and computational analyses of protein oxidative modification.<\/jats:p>\n               <jats:p>Availability: The database is freely available at: http:\/\/biocomputer.bio.cuhk.edu.hk\/RedoxDB.<\/jats:p>\n               <jats:p>Contact: \u00a0djguo@cuhk.edu.hk<\/jats:p>\n               <jats:p>Supplementary Information: \u00a0Supplementary data are available at Bioinformatics Online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts468","type":"journal-article","created":{"date-parts":[[2012,7,26]],"date-time":"2012-07-26T03:24:31Z","timestamp":1343273071000},"page":"2551-2552","source":"Crossref","is-referenced-by-count":65,"title":["RedoxDB\u2014a curated database for experimentally verified protein oxidative modification"],"prefix":"10.1093","volume":"28","author":[{"given":"Ming-an","family":"Sun","sequence":"first","affiliation":[{"name":"School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yejun","family":"Wang","sequence":"additional","affiliation":[{"name":"School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Han","family":"Cheng","sequence":"additional","affiliation":[{"name":"School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Qing","family":"Zhang","sequence":"additional","affiliation":[{"name":"School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wei","family":"Ge","sequence":"additional","affiliation":[{"name":"School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dianjing","family":"Guo","sequence":"additional","affiliation":[{"name":"School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2012,7,25]]},"reference":[{"key":"2023012513141001600_bts468-B1","doi-asserted-by":"crossref","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","article-title":"Gapped BLAST and PSI-BLAST: a new generation of protein database search programs","volume":"25","author":"Altschul","year":"1997","journal-title":"Nucleic Acids Res."},{"key":"2023012513141001600_bts468-B2","doi-asserted-by":"crossref","first-page":"1049","DOI":"10.1089\/ars.2010.3400","article-title":"Thiol-based redox switches and gene regulation","volume":"14","author":"Antelmann","year":"2011","journal-title":"Antioxid. Redox Signal."},{"key":"2023012513141001600_bts468-B3","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1089\/ars.2007.9.1","article-title":"Protein tyrosine phosphorylation and reversible oxidation: two cross-talking posttranslation modifications","volume":"9","author":"Chiarugi","year":"2007","journal-title":"Antioxid. Redox Signal."},{"key":"2023012513141001600_bts468-B4","doi-asserted-by":"crossref","first-page":"120","DOI":"10.1016\/j.cbpa.2010.11.003","article-title":"Proteomic approaches to the characterization of protein thiol modification","volume":"15","author":"Chouchani","year":"2011","journal-title":"Curr. Opin. Chem. Biol."},{"key":"2023012513141001600_bts468-B5","doi-asserted-by":"crossref","first-page":"387","DOI":"10.1126\/science.1133114","article-title":"High-throughput identification of catalytic redox-active cysteine residues","volume":"315","author":"Fomenko","year":"2007","journal-title":"Science (New York, NY)"},{"key":"2023012513141001600_bts468-B6","doi-asserted-by":"crossref","first-page":"835","DOI":"10.1021\/bi9020378","article-title":"Signaling functions of reactive oxygen species","volume":"49","author":"Forman","year":"2010","journal-title":"Biochemistry"},{"key":"2023012513141001600_bts468-B7","doi-asserted-by":"crossref","first-page":"395","DOI":"10.1146\/annurev.micro.57.030502.090938","article-title":"Pathways of oxidative damage","volume":"57","author":"Imlay","year":"2003","journal-title":"Annu. Rev. Microbiol."},{"key":"2023012513141001600_bts468-B8","doi-asserted-by":"crossref","first-page":"2581","DOI":"10.1089\/ars.2010.3551","article-title":"The disulfide proteome and other reactive cysteine proteomes: analysis and functional significance","volume":"14","author":"Lindahl","year":"2011","journal-title":"Antioxid. Redox Signal."},{"key":"2023012513141001600_bts468-B9","doi-asserted-by":"crossref","first-page":"e1000383","DOI":"10.1371\/journal.pcbi.1000383","article-title":"A structure-based approach for detection of thiol oxidoreductases and their catalytic redox-active cysteine residues","volume":"5","author":"Marino","year":"2009","journal-title":"PLoS Comput. Biol."},{"key":"2023012513141001600_bts468-B10","doi-asserted-by":"crossref","first-page":"335","DOI":"10.1146\/annurev-genet-102108-134201","article-title":"Thioredoxins and glutaredoxins: unifying elements in redox biology","volume":"43","author":"Meyer","year":"2009","journal-title":"Annu. Rev. Genet."},{"key":"2023012513141001600_bts468-B11","doi-asserted-by":"crossref","first-page":"746","DOI":"10.1016\/j.cbpa.2008.07.028","article-title":"Expanding the functional diversity of proteins through cysteine oxidation","volume":"12","author":"Reddie","year":"2008","journal-title":"Curr. Opin. Chem. Biol."},{"key":"2023012513141001600_bts468-B12","doi-asserted-by":"crossref","first-page":"473","DOI":"10.1110\/ps.073252408","article-title":"Prediction of reversibly oxidized protein cysteine thiols using protein structure properties","volume":"17","author":"Sanchez","year":"2008","journal-title":"Protein Sci."},{"key":"2023012513141001600_bts468-B13","doi-asserted-by":"crossref","first-page":"2985","DOI":"10.1089\/ars.2009.2513","article-title":"Redox control of the cell cycle in health and disease","volume":"11","author":"Sarsour","year":"2009","journal-title":"Antioxid. Redox Signal."},{"key":"2023012513141001600_bts468-B14","doi-asserted-by":"crossref","first-page":"790","DOI":"10.1038\/nature09472","article-title":"Quantitative reactivity profiling predicts functional cysteines in proteomes","volume":"468","author":"Weerapana","year":"2010","journal-title":"Nature"},{"key":"2023012513141001600_bts468-B15","doi-asserted-by":"crossref","first-page":"245","DOI":"10.1093\/nar\/30.1.245","article-title":"The Protein Data Bank: unifying the archive","volume":"30","author":"Westbrook","year":"2002","journal-title":"Nucleic Acids Res."},{"key":"2023012513141001600_bts468-B16","doi-asserted-by":"crossref","first-page":"D187","DOI":"10.1093\/nar\/gkj161","article-title":"The Universal Protein Resource (UniProt): an expanding universe of protein information","volume":"34","author":"Wu","year":"2006","journal-title":"Nucleic Acids Res."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/28\/19\/2551\/48875032\/bioinformatics_28_19_2551.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/28\/19\/2551\/48875032\/bioinformatics_28_19_2551.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T19:15:29Z","timestamp":1674674129000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/28\/19\/2551\/289097"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2012,7,25]]},"references-count":16,"journal-issue":{"issue":"19","published-print":{"date-parts":[[2012,10,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bts468","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2012,10,1]]},"published":{"date-parts":[[2012,7,25]]}}}