{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,13]],"date-time":"2026-05-13T09:09:45Z","timestamp":1778663385414,"version":"3.51.4"},"reference-count":43,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":2131,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,2,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Predicting protein interactions involving peptide recognition domains is essential for understanding the many important biological processes they mediate. It is important to consider the binding strength of these interactions to help us construct more biologically relevant protein interaction networks that consider cellular context and competition between potential binders.<\/jats:p>\n               <jats:p>Results: We developed a novel regression framework that considers both positive (quantitative) and negative (qualitative) interaction data available for mouse PDZ domains to quantitatively predict interactions between PDZ domains, a large peptide recognition domain family, and their peptide ligands using primary sequence information. First, we show that it is possible to learn from existing quantitative and negative interaction data to infer the relative binding strength of interactions involving previously unseen PDZ domains and\/or peptides given their primary sequence. Performance was measured using cross-validated hold out testing and testing with previously unseen PDZ domain\u2013peptide interactions. Second, we find that incorporating negative data improves quantitative interaction prediction. Third, we show that sequence similarity is an important prediction performance determinant, which suggests that experimentally collecting additional quantitative interaction data for underrepresented PDZ domain subfamilies will improve prediction.<\/jats:p>\n               <jats:p>Availability and Implementation: The Matlab code for our SemiSVR predictor and all data used here are available at http:\/\/baderlab.org\/Data\/PDZAffinity.<\/jats:p>\n               <jats:p>Contact: \u00a0gary.bader@utoronto.ca; dengnaiyang@cau.edu.cn<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq657","type":"journal-article","created":{"date-parts":[[2010,12,3]],"date-time":"2010-12-03T01:53:52Z","timestamp":1291341232000},"page":"383-390","source":"Crossref","is-referenced-by-count":26,"title":["A regression framework incorporating quantitative and negative interaction data improves quantitative prediction of PDZ domain\u2013peptide interaction from primary sequence"],"prefix":"10.1093","volume":"27","author":[{"given":"Xiaojian","family":"Shao","sequence":"first","affiliation":[{"name":"1 Department of Applied Mathematics, College of Science, China Agricultural University, Beijing, 100083, China, 2Banting and Best Department of Medical Research, University of Toronto, Donnelly Centre for Cellular and Biomolecular Research, Toronto, ON M5S 3E1, 3Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada and 4Department of Biochemistry, University of Western Ontario, London, ON N6A 5B8, Canada"},{"name":"1 Department of Applied Mathematics, College of Science, China Agricultural University, Beijing, 100083, China, 2Banting and Best Department of Medical Research, University of Toronto, Donnelly Centre for Cellular and Biomolecular Research, Toronto, ON M5S 3E1, 3Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada and 4Department of Biochemistry, University of Western Ontario, London, ON N6A 5B8, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chris S. H.","family":"Tan","sequence":"additional","affiliation":[{"name":"1 Department of Applied Mathematics, College of Science, China Agricultural University, Beijing, 100083, China, 2Banting and Best Department of Medical Research, University of Toronto, Donnelly Centre for Cellular and Biomolecular Research, Toronto, ON M5S 3E1, 3Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada and 4Department of Biochemistry, University of Western Ontario, London, ON N6A 5B8, Canada"},{"name":"1 Department of Applied Mathematics, College of Science, China Agricultural University, Beijing, 100083, China, 2Banting and Best Department of Medical Research, University of Toronto, Donnelly Centre for Cellular and Biomolecular Research, Toronto, ON M5S 3E1, 3Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada and 4Department of Biochemistry, University of Western Ontario, London, ON N6A 5B8, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Courtney","family":"Voss","sequence":"additional","affiliation":[{"name":"1 Department of Applied Mathematics, College of Science, China Agricultural University, Beijing, 100083, China, 2Banting and Best Department of Medical Research, University of Toronto, Donnelly Centre for Cellular and Biomolecular Research, Toronto, ON M5S 3E1, 3Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada and 4Department of Biochemistry, University of Western Ontario, London, ON N6A 5B8, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shawn S. C.","family":"Li","sequence":"additional","affiliation":[{"name":"1 Department of Applied Mathematics, College of Science, China Agricultural University, Beijing, 100083, China, 2Banting and Best Department of Medical Research, University of Toronto, Donnelly Centre for Cellular and Biomolecular Research, Toronto, ON M5S 3E1, 3Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada and 4Department of Biochemistry, University of Western Ontario, London, ON N6A 5B8, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Naiyang","family":"Deng","sequence":"additional","affiliation":[{"name":"1 Department of Applied Mathematics, College of Science, China Agricultural University, Beijing, 100083, China, 2Banting and Best Department of Medical Research, University of Toronto, Donnelly Centre for Cellular and Biomolecular Research, Toronto, ON M5S 3E1, 3Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada and 4Department of Biochemistry, University of Western Ontario, London, ON N6A 5B8, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gary D.","family":"Bader","sequence":"additional","affiliation":[{"name":"1 Department of Applied Mathematics, College of Science, China Agricultural University, Beijing, 100083, China, 2Banting and Best Department of Medical Research, University of Toronto, Donnelly Centre for Cellular and Biomolecular Research, Toronto, ON M5S 3E1, 3Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada and 4Department of Biochemistry, University of Western Ontario, London, ON N6A 5B8, Canada"},{"name":"1 Department of Applied Mathematics, College of Science, China Agricultural University, Beijing, 100083, China, 2Banting and Best Department of Medical Research, University of Toronto, Donnelly Centre for Cellular and Biomolecular Research, Toronto, ON M5S 3E1, 3Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada and 4Department of Biochemistry, University of Western Ontario, London, ON N6A 5B8, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2010,12,2]]},"reference":[{"key":"2023012511541748700_B1","doi-asserted-by":"crossref","first-page":"6395","DOI":"10.1073\/pnas.0408677102","article-title":"Solving the protein sequence metric problem","volume":"102","author":"Atchley","year":"2005","journal-title":"Proc Natl Assoc Sci. 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