{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,5]],"date-time":"2026-05-05T16:29:28Z","timestamp":1777998568916,"version":"3.51.4"},"reference-count":22,"publisher":"World Scientific Pub Co Pte Ltd","issue":"04","funder":[{"name":"National Health and Medical Research Council of Australia","award":["1144652 and 1127948"],"award-info":[{"award-number":["1144652 and 1127948"]}]},{"name":"Young Scientists Fund of the National Natural Science Foundation of ChinaYoung Scientists Fund of the National Natural Science Foundation of China","award":["31701142"],"award-info":[{"award-number":["31701142"]}]},{"DOI":"10.13039\/501100000923","name":"Australian Research Council","doi-asserted-by":"crossref","award":["LP110200333"],"award-info":[{"award-number":["LP110200333"]}],"id":[{"id":"10.13039\/501100000923","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100000923","name":"Australian Research Council","doi-asserted-by":"crossref","award":["DP120104460"],"award-info":[{"award-number":["DP120104460"]}],"id":[{"id":"10.13039\/501100000923","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["J. Bioinform. Comput. Biol."],"published-print":{"date-parts":[[2020,8]]},"abstract":"<jats:p>Background: Phosphorylation of histidine residues plays crucial roles in signaling pathways and cell metabolism in prokaryotes such as bacteria. While evidence has emerged that protein histidine phosphorylation also occurs in more complex organisms, its role in mammalian cells has remained largely uncharted. Thus, it is highly desirable to develop computational tools that are able to identify histidine phosphorylation sites. Result: Here, we introduce PROSPECT that enables fast and accurate prediction of proteome-wide histidine phosphorylation substrates and sites. Our tool is based on a hybrid method that integrates the outputs of two convolutional neural network (CNN)-based classifiers and a random forest-based classifier. Three features, including the one-of-K coding, enhanced grouped amino acids content (EGAAC) and composition of k-spaced amino acid group pairs (CKSAAGP) encoding, were taken as the input to three classifiers, respectively. Our results show that it is able to accurately predict histidine phosphorylation sites from sequence information. Our PROSPECT web server is user-friendly and publicly available at http:\/\/PROSPECT.erc.monash.edu\/ . Conclusions: PROSPECT is superior than other pHis predictors in both the running speed and prediction accuracy and we anticipate that the PROSPECT webserver will become a popular tool for identifying the pHis sites in bacteria.<\/jats:p>","DOI":"10.1142\/s0219720020500183","type":"journal-article","created":{"date-parts":[[2020,3,30]],"date-time":"2020-03-30T07:11:20Z","timestamp":1585552280000},"page":"2050018","source":"Crossref","is-referenced-by-count":29,"title":["PROSPECT: A web server for predicting protein histidine phosphorylation sites"],"prefix":"10.1142","volume":"18","author":[{"given":"Zhen","family":"Chen","sequence":"first","affiliation":[{"name":"School of Basic Medical Science, Qingdao University, Qingdao, P.\u00a0R.\u00a0China"},{"name":"State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese, Academy of Agricultural Sciences (CAAS), Anyang, P.\u00a0R.\u00a0China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pei","family":"Zhao","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese, Academy of Agricultural Sciences (CAAS), Anyang, P.\u00a0R.\u00a0China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Fuyi","family":"Li","sequence":"additional","affiliation":[{"name":"Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Australia"},{"name":"Monash Centre for Data Science, Faculty of Information Technology, Monash University, VIC 3800, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Andr\u00e9","family":"Leier","sequence":"additional","affiliation":[{"name":"Department of Genetics, School of Medicine, University of Alabama at Birmingham, USA"},{"name":"Informatics Institute, School of Medicine, University of Alabama at Birmingham, 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