{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,25]],"date-time":"2026-03-25T10:50:50Z","timestamp":1774435850718,"version":"3.50.1"},"reference-count":109,"publisher":"Oxford University Press (OUP)","issue":"20","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,10,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivation: Sumoylation is a post-translational modification (PTM) process, in which small ubiquitin-related modifier (SUMO) is attaching by covalent bonds to substrate protein. It is critical to many different biological processes such as replicating genome, expressing gene, localizing and stabilizing proteins; unfortunately, it is also involved with many major disorders including Alzheimer\u2019s and Parkinson\u2019s diseases. Therefore, for both basic research and drug development, it is important to identify the sumoylation sites in proteins.<\/jats:p><jats:p>Results: To address such a problem, we developed a predictor called pSumo-CD by incorporating the sequence-coupled information into the general pseudo-amino acid composition (PseAAC) and introducing the covariance discriminant (CD) algorithm, in which a bias-adjustment term, which has the function to automatically adjust the errors caused by the bias due to the imbalance of training data, had been incorporated. Rigorous cross-validations indicated that the new predictor remarkably outperformed the existing state-of-the-art prediction method for the same purpose.<\/jats:p><jats:p>Availability and implementation: For the convenience of most experimental scientists, a user-friendly web-server for pSumo-CD has been established at http:\/\/www.jci-bioinfo.cn\/pSumo-CD, by which users can easily obtain their desired results without the need to go through the complicated mathematical equations involved.<\/jats:p><jats:p>Contact: jjia@gordonlifescience.org, xxiao@gordonlifescience.org or kcchou@gordonlifescience.org<\/jats:p><jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btw387","type":"journal-article","created":{"date-parts":[[2016,6,29]],"date-time":"2016-06-29T14:57:42Z","timestamp":1467212262000},"page":"3133-3141","source":"Crossref","is-referenced-by-count":174,"title":["pSumo-CD: predicting sumoylation sites in proteins with covariance discriminant algorithm by incorporating sequence-coupled effects into general PseAAC"],"prefix":"10.1093","volume":"32","author":[{"given":"Jianhua","family":"Jia","sequence":"first","affiliation":[{"name":"1 Computer Department, Jing-De-Zhen Ceramic Institute, Jing-De-Zhen 333403, China"},{"name":"2 Gordon Life Science Institute, Boston, MA 02478, USA"}]},{"given":"Liuxia","family":"Zhang","sequence":"additional","affiliation":[{"name":"1 Computer Department, Jing-De-Zhen Ceramic Institute, Jing-De-Zhen 333403, China"}]},{"given":"Zi","family":"Liu","sequence":"additional","affiliation":[{"name":"3 School of Computer Science and Engineering, Nanjing University of Science and Technology, Nanjing 210094, China"}]},{"given":"Xuan","family":"Xiao","sequence":"additional","affiliation":[{"name":"1 Computer Department, Jing-De-Zhen Ceramic Institute, Jing-De-Zhen 333403, China"},{"name":"2 Gordon Life Science Institute, Boston, MA 02478, USA"}]},{"given":"Kuo-Chen","family":"Chou","sequence":"additional","affiliation":[{"name":"2 Gordon Life Science Institute, Boston, MA 02478, USA"},{"name":"4 Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah 21589, Saudi Arabia"},{"name":"5 Center of Bioinformatics, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China"}]}],"member":"286","published-online":{"date-parts":[[2016,6,26]]},"reference":[{"key":"2023020113443153300_btw387-B1","doi-asserted-by":"crossref","DOI":"10.1007\/s00232-015-9868-8","article-title":"Prediction of protein submitochondrial locations by incorporating dipeptide composition into Chou's general pseudo amino acid composition","author":"Ahmad","year":"2016","journal-title":"J. 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