{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,8]],"date-time":"2025-11-08T12:11:20Z","timestamp":1762603880423},"reference-count":29,"publisher":"Oxford University Press (OUP)","issue":"12","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,6,15]]},"abstract":"<jats:p>Motivation: \u00a0In silico prediction of site-specific kinase\u2013substrate relationships (ssKSRs) is crucial for deciphering phosphorylation networks by linking kinomes to phosphoproteomes. However, currently available predictors for ssKSRs give rise to a large number of false-positive results because they use only a short sequence stretch around phosphosite as determinants of kinase specificity and do not consider the biological context of kinase\u2013substrate recognition.<\/jats:p>\n               <jats:p>Results: Based on the analysis of domain-specific kinase\u2013substrate relationships, we have constructed a domain-level phosphorylation network that implicitly incorporates various contextual factors. It reveals preferential phosphorylation of specific domains by certain kinases. These novel correlations have been implemented in PhosNetConstruct, an automated program for predicting target kinases for a substrate protein. PhosNetConstruct distinguishes cognate kinase\u2013substrate pairs from a large number of non-cognate combinations. Benchmarking on independent datasets using various statistical measures demonstrates the superior performance of PhosNetConstruct over ssKSR-based predictors.<\/jats:p>\n               <jats:p>Availability and implementation: PhosNetConstruct is freely available at http:\/\/www.nii.ac.in\/phosnetconstruct.html.<\/jats:p>\n               <jats:p>Contact: \u00a0deb@nii.res.in<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary Data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu112","type":"journal-article","created":{"date-parts":[[2014,2,27]],"date-time":"2014-02-27T01:26:41Z","timestamp":1393464401000},"page":"1730-1738","source":"Crossref","is-referenced-by-count":15,"title":["Deciphering kinase\u2013substrate relationships by analysis of domain-specific phosphorylation network"],"prefix":"10.1093","volume":"30","author":[{"given":"Nikhil Prakash","family":"Damle","sequence":"first","affiliation":[{"name":"1Bioinformatics Centre, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India"}]},{"given":"Debasisa","family":"Mohanty","sequence":"additional","affiliation":[{"name":"1Bioinformatics Centre, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India"}]}],"member":"286","published-online":{"date-parts":[[2014,2,25]]},"reference":[{"key":"2023012711061657200_btu112-B1","doi-asserted-by":"crossref","first-page":"1633","DOI":"10.1002\/pmic.200300771","article-title":"Prediction of post-translational glycosylation and phosphorylation of proteins from the amino acid sequence","volume":"4","author":"Blom","year":"2004","journal-title":"Proteomics"},{"key":"2023012711061657200_btu112-B2","doi-asserted-by":"crossref","first-page":"307","DOI":"10.1007\/978-1-60761-977-2_19","article-title":"Phosphoproteome resource for systems biology research","volume":"694","author":"Bodenmiller","year":"2011","journal-title":"Methods Mol. 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