{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,13]],"date-time":"2026-07-13T16:33:14Z","timestamp":1783960394121,"version":"3.55.0"},"reference-count":38,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2021,10,20]],"date-time":"2021-10-20T00:00:00Z","timestamp":1634688000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32088101"],"award-info":[{"award-number":["32088101"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31871341"],"award-info":[{"award-number":["31871341"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2020YFE0202200"],"award-info":[{"award-number":["2020YFE0202200"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100017616","name":"Beijing Talents Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100017616","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,1,7]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>As an important post-translational modification, ubiquitination mediates \u223c80% of protein degradation in eukaryotes. The degree of protein ubiquitination is tightly determined by the delicate balance between specific ubiquitin ligase (E3)-mediated ubiquitination and deubiquitinase-mediated deubiquitination. In 2017, we developed UbiBrowser 1.0, which is an integrated database for predicted\u00a0human proteome-wide E3\u2013substrate interactions. Here, to meet the urgent requirement of proteome-wide E3\/deubiquitinase\u2013substrate interactions (ESIs\/DSIs) in multiple organisms, we updated UbiBrowser to version 2.0 (http:\/\/ubibrowser.ncpsb.org.cn). Using an improved protocol, we collected 4068\/967 known ESIs\/DSIs by manual curation, and we predicted about 2.2 million highly confident ESIs\/DSIs in 39 organisms, with\u00a0&amp;gt;210-fold increase in total data volume. In addition, we made several new features in the updated version: (i) it allows exploring proteins\u2019 upstream E3 ligases and deubiquitinases simultaneously; (ii) it has significantly increased species coverage; (iii) it presents a uniform confidence scoring system to rank predicted ESIs\/DSIs. To facilitate the usage of UbiBrowser 2.0, we also redesigned the web interface for exploring these known and predicted ESIs\/DSIs, and added functions of \u2018Browse\u2019, \u2018Download\u2019 and \u2018Application Programming Interface\u2019. We believe that UbiBrowser 2.0, as a discovery tool, will contribute to the study of protein ubiquitination and the development of drug targets for complex diseases.<\/jats:p>","DOI":"10.1093\/nar\/gkab962","type":"journal-article","created":{"date-parts":[[2021,10,6]],"date-time":"2021-10-06T00:58:38Z","timestamp":1633481918000},"page":"D719-D728","source":"Crossref","is-referenced-by-count":201,"title":["UbiBrowser 2.0: a comprehensive resource for proteome-wide known and predicted ubiquitin ligase\/deubiquitinase\u2013substrate interactions in eukaryotic species"],"prefix":"10.1093","volume":"50","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4559-5450","authenticated-orcid":false,"given":"Xun","family":"Wang","sequence":"first","affiliation":[{"name":"State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2009-7079","authenticated-orcid":false,"given":"Yang","family":"Li","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mengqi","family":"He","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiangren","family":"Kong","sequence":"additional","affiliation":[{"name":"College of Life Sciences, Hebei University, Baoding 071002, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peng","family":"Jiang","sequence":"additional","affiliation":[{"name":"School of Basic Medical Sciences, Anhui Medical University, Hefei\u00a0230032, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xi","family":"Liu","sequence":"additional","affiliation":[{"name":"College of Life Sciences, Hebei University, Baoding 071002, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lihong","family":"Diao","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xinlei","family":"Zhang","sequence":"additional","affiliation":[{"name":"Beijing Geneworks Technology Co.,Ltd., Beijing 100101, 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071002, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2866-4904","authenticated-orcid":false,"given":"Yuan","family":"Liu","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chun-Ping","family":"Cui","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yan","family":"Wang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Liujun","family":"Tang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lingqiang","family":"Zhang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China"},{"name":"School of Basic Medical Sciences, Anhui Medical University, Hefei\u00a0230032, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fuchu","family":"He","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing 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