{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,22]],"date-time":"2025-02-22T00:44:50Z","timestamp":1740185090186,"version":"3.37.3"},"reference-count":46,"publisher":"Oxford University Press (OUP)","issue":"22","license":[{"start":{"date-parts":[[2018,6,1]],"date-time":"2018-06-01T00:00:00Z","timestamp":1527811200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/100000001","name":"National Science Foundation IOS","doi-asserted-by":"crossref","award":["1021795","1656510"],"award-info":[{"award-number":["1021795","1656510"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Vermont Genetics Network"},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["8P20GM103449"],"award-info":[{"award-number":["8P20GM103449"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"name":"INBRE"},{"DOI":"10.13039\/100000057","name":"NIGMS","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["5P20RR016435"],"award-info":[{"award-number":["5P20RR016435"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"name":"COBRE"},{"DOI":"10.13039\/100000057","name":"NIGMS","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,11,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>The development of proteomic methods for the characterization of domain\/motif interactions has greatly expanded our understanding of signal transduction. However, proteomics-based binding screens have limitations including that the queried tissue or cell type may not harbor all potential interacting partners or post-translational modifications (PTMs) required for the interaction. Therefore, we sought a generalizable, complementary in silico approach to identify potentially novel motif and PTM-dependent binding partners of high priority.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We used as an initial example the interaction between the Src homology 2 (SH2) domains of the adaptor proteins CT10 regulator of kinase (CRK) and CRK-like (CRKL) and phosphorylated-YXXP motifs. Employing well-curated, publicly-available resources, we scored and prioritized potential CRK\/CRKL\u2013SH2 interactors possessing signature characteristics of known interacting partners. Our approach gave high priority scores to 102 of the &amp;gt;9000 YXXP motif-containing proteins. Within this 102 were 21 of the 25 curated CRK\/CRKL\u2013SH2-binding partners showing a more than 80-fold enrichment. Several predicted interactors were validated biochemically. To demonstrate generalized applicability, we used our workflow to predict protein\u2013protein interactions dependent upon motif-specific arginine methylation. Our data demonstrate the applicability of our approach to, conceivably, any modular binding domain that recognizes a specific post-translationally modified motif.<\/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\/bty434","type":"journal-article","created":{"date-parts":[[2018,5,25]],"date-time":"2018-05-25T03:11:41Z","timestamp":1527217901000},"page":"3898-3906","source":"Crossref","is-referenced-by-count":2,"title":["An <i>in silico<\/i> proteomics screen to predict and prioritize protein\u2013protein interactions dependent on post-translationally modified motifs"],"prefix":"10.1093","volume":"34","author":[{"given":"Anna M","family":"Schmoker","sequence":"first","affiliation":[{"name":"Department of Biology, University of Vermont, Burlington, VT, USA"}]},{"given":"Heather E","family":"Driscoll","sequence":"additional","affiliation":[{"name":"Vermont Genetics Network Bioinformatics Core, University of Vermont, Burlington, VT, USA"},{"name":"Department of Biology, Norwich University, Northfield, VT, USA"}]},{"given":"Stefanie R","family":"Geiger","sequence":"additional","affiliation":[{"name":"Department of Biology, University of Vermont, Burlington, VT, USA"}]},{"given":"James J","family":"Vincent","sequence":"additional","affiliation":[{"name":"Department of Biology, University of Vermont, Burlington, VT, USA"},{"name":"Vermont Genetics Network Bioinformatics Core, University of Vermont, Burlington, VT, USA"}]},{"given":"Alicia M","family":"Ebert","sequence":"additional","affiliation":[{"name":"Department of Biology, University of Vermont, Burlington, VT, USA"}]},{"given":"Bryan A","family":"Ballif","sequence":"additional","affiliation":[{"name":"Department of Biology, University of Vermont, Burlington, VT, USA"}]}],"member":"286","published-online":{"date-parts":[[2018,6,1]]},"reference":[{"key":"2023012712345256100_bty434-B1","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1016\/S0960-9822(02)01397-0","article-title":"Fyn tyrosine kinase is a critical regulator of disabled-1 during brain development","volume":"13","author":"Arnaud","year":"2003","journal-title":"Curr. 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