{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,20]],"date-time":"2026-06-20T17:58:16Z","timestamp":1781978296824,"version":"3.54.5"},"reference-count":49,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2016,12,13]],"date-time":"2016-12-13T00:00:00Z","timestamp":1481587200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"DOI":"10.13039\/501100001868","name":"National Science Council of Taiwan","doi-asserted-by":"crossref","award":["MOST-105-2221-E-009-138-MY2"],"award-info":[{"award-number":["MOST-105-2221-E-009-138-MY2"]}],"id":[{"id":"10.13039\/501100001868","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100001868","name":"National Science Council of Taiwan","doi-asserted-by":"crossref","award":["MOST-105-2627-M-009-008"],"award-info":[{"award-number":["MOST-105-2627-M-009-008"]}],"id":[{"id":"10.13039\/501100001868","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Center for Bioinformatics Research of Aiming","award":["104W962"],"award-info":[{"award-number":["104W962"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,3,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Numerous ubiquitination sites remain undiscovered because of the limitations of mass spectrometry-based methods. Existing prediction methods use randomly selected non-validated sites as non-ubiquitination sites to train ubiquitination site prediction models.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We propose an evolutionary screening algorithm (ESA) to select effective negatives among non-validated sites and an ESA-based prediction method, ESA-UbiSite, to identify human ubiquitination sites. The ESA selects non-validated sites least likely to be ubiquitination sites as training negatives. Moreover, the ESA and ESA-UbiSite use a set of well-selected physicochemical properties together with a support vector machine for accurate prediction. Experimental results show that ESA-UbiSite with effective negatives achieved 0.92 test accuracy and a Matthews\u2019s correlation coefficient of 0.48, better than existing prediction methods. The ESA increased ESA-UbiSite\u2019s test accuracy from 0.75 to 0.92 and can improve other post-translational modification site prediction methods.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and Implementation<\/jats:title>\n                  <jats:p>An ESA-UbiSite-based web server has been established at http:\/\/iclab.life.nctu.edu.tw\/iclab_webtools\/ESAUbiSite\/.<\/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\/btw701","type":"journal-article","created":{"date-parts":[[2016,11,8]],"date-time":"2016-11-08T12:05:48Z","timestamp":1478606748000},"page":"661-668","source":"Crossref","is-referenced-by-count":43,"title":["ESA-UbiSite: accurate prediction of human ubiquitination sites by identifying a set of effective negatives"],"prefix":"10.1093","volume":"33","author":[{"given":"Jyun-Rong","family":"Wang","sequence":"first","affiliation":[{"name":"Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wen-Lin","family":"Huang","sequence":"additional","affiliation":[{"name":"Department and Institute of Industrial Engineering and Management, Minghsin University of Science and Technology, Hsinchu, Taiwan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ming-Ju","family":"Tsai","sequence":"additional","affiliation":[{"name":"Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kai-Ti","family":"Hsu","sequence":"additional","affiliation":[{"name":"Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hui-Ling","family":"Huang","sequence":"additional","affiliation":[{"name":"Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan"},{"name":"Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shinn-Ying","family":"Ho","sequence":"additional","affiliation":[{"name":"Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan"},{"name":"Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2016,12,13]]},"reference":[{"key":"2023020204424485300_btw701-B1","doi-asserted-by":"crossref","first-page":"789","DOI":"10.1093\/nar\/gkp1066","article-title":"The hydrophobic patch of ubiquitin is required to protect transactivator-promoter complexes from destabilization by the proteasomal ATPases","volume":"38","author":"Archer","year":"2010","journal-title":"Nucleic Acids Res"},{"key":"2023020204424485300_btw701-B2","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1038\/35050524","article-title":"Hrd1p\/Der3p is a membrane-anchored ubiquitin ligase required for ER-associated degradation","volume":"3","author":"Bays","year":"2001","journal-title":"Nat. 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