{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,8,4]],"date-time":"2024-08-04T06:40:22Z","timestamp":1722753622411},"reference-count":13,"publisher":"Oxford University Press (OUP)","issue":"18","license":[{"start":{"date-parts":[[2016,11,14]],"date-time":"2016-11-14T00:00:00Z","timestamp":1479081600000},"content-version":"vor","delay-in-days":901,"URL":"http:\/\/creativecommons.org\/licenses\/by\/3.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,9,15]]},"abstract":"Abstract<\/jats:title>\n Summary : MoDPepInt (Modular Domain Peptide Interaction) is a new easy-to-use web server for the prediction of binding partners for modular protein domains. Currently, we offer models for SH2, SH3 and PDZ domains via the tools SH2PepInt, SH3PepInt and PDZPepInt, respectively. More specifically, our server offers predictions for 51 SH2 human domains and 69 SH3 human domains via single domain models, and predictions for 226 PDZ domains across several species, via 43 multidomain models. All models are based on support vector machines with different kernel functions ranging from polynomial, to Gaussian, to advanced graph kernels. In this way, we model non-linear interactions between amino acid residues. Results were validated on manually curated datasets achieving competitive performance against various state-of-the-art approaches.<\/jats:p>\n Availability and implementation: The MoDPepInt server is available under the URL http:\/\/modpepint.informatik.uni-freiburg.de\/<\/jats:p>\n Contact : backofen@informatik.uni-freiburg.de<\/jats:p>\n Supplementary information : Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu350","type":"journal-article","created":{"date-parts":[[2014,5,29]],"date-time":"2014-05-29T03:33:46Z","timestamp":1401334426000},"page":"2668-2669","source":"Crossref","is-referenced-by-count":37,"title":["MoDPepInt: an interactive web server for prediction of modular domain\u2013peptide interactions"],"prefix":"10.1093","volume":"30","author":[{"given":"Kousik","family":"Kundu","sequence":"first","affiliation":[{"name":"1 Bioinformatics Group, Department of Computer Science, 79110 Freiburg and 2 Centre for Biological Signalling Studies (BIOSS), 79104 Freiburg, University of Freiburg, Germany"}]},{"given":"Martin","family":"Mann","sequence":"additional","affiliation":[{"name":"1 Bioinformatics Group, Department of Computer Science, 79110 Freiburg and 2 Centre for Biological Signalling Studies (BIOSS), 79104 Freiburg, University of Freiburg, Germany"}]},{"given":"Fabrizio","family":"Costa","sequence":"additional","affiliation":[{"name":"1 Bioinformatics Group, Department of Computer Science, 79110 Freiburg and 2 Centre for Biological Signalling Studies (BIOSS), 79104 Freiburg, University of Freiburg, Germany"}]},{"given":"Rolf","family":"Backofen","sequence":"additional","affiliation":[{"name":"1 Bioinformatics Group, Department of Computer Science, 79110 Freiburg and 2 Centre for Biological Signalling Studies (BIOSS), 79104 Freiburg, University of Freiburg, Germany"},{"name":"1 Bioinformatics Group, Department of Computer Science, 79110 Freiburg and 2 Centre for Biological Signalling Studies (BIOSS), 79104 Freiburg, University of Freiburg, Germany"}]}],"member":"286","published-online":{"date-parts":[[2014,5,28]]},"reference":[{"key":"2023012711554646300_btu350-B1","doi-asserted-by":"crossref","first-page":"e1002341","DOI":"10.1371\/journal.pcbi.1002341","article-title":"A dynamic view of domain-motif interactions","volume":"8","author":"Akiva","year":"2012","journal-title":"PLoS Comput. Biol."},{"key":"2023012711554646300_btu350-B2","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1038\/75556","article-title":"Gene ontology: tool for the unification of biology. The Gene Ontology Consortium","volume":"25","author":"Ashburner","year":"2000","journal-title":"Nat. Genet."},{"key":"2023012711554646300_btu350-B3","doi-asserted-by":"crossref","first-page":"313","DOI":"10.1006\/jmbi.2000.3670","article-title":"SH3-SPOT: an algorithm to predict preferred ligands to different members of the SH3 gene family","volume":"298","author":"Brannetti","year":"2000","journal-title":"J. Mol. Biol."},{"key":"2023012711554646300_btu350-B4","doi-asserted-by":"crossref","first-page":"4","DOI":"10.1016\/j.biotechadv.2011.06.012","article-title":"The protein interaction network mediated by human SH3 domains","volume":"30","author":"Carducci","year":"2012","journal-title":"Biotechnol. Adv."},{"key":"2023012711554646300_btu350-B5","doi-asserted-by":"crossref","first-page":"3433","DOI":"10.1093\/bioinformatics\/bti541","article-title":"IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content","volume":"21","author":"Dosztanyi","year":"2005","journal-title":"Bioinformatics"},{"key":"2023012711554646300_btu350-B6","doi-asserted-by":"crossref","first-page":"D261","DOI":"10.1093\/nar\/gkr1122","article-title":"PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse","volume":"40","author":"Hornbeck","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"2023012711554646300_btu350-B7","doi-asserted-by":"crossref","first-page":"1201","DOI":"10.1016\/j.jmb.2007.12.054","article-title":"Characterization of domain-peptide interaction interface: a case study on the amphiphysin-1 SH3 domain","volume":"376","author":"Hou","year":"2008","journal-title":"J. Mol. Biol."},{"key":"2023012711554646300_btu350-B8","doi-asserted-by":"crossref","first-page":"2982","DOI":"10.1021\/pr3000688","article-title":"Characterization of domain-peptide interaction interface: prediction of SH3 domain-mediated protein-protein interaction network in yeast by generic structure-based models","volume":"11","author":"Hou","year":"2012","journal-title":"J. Proteome Res."},{"key":"2023012711554646300_btu350-B9","doi-asserted-by":"crossref","first-page":"i335","DOI":"10.1093\/bioinformatics\/btt220","article-title":"A graph kernel approach for alignment-free domain-peptide interaction prediction with an application to human SH3 domains","volume":"29","author":"Kundu","year":"2013","journal-title":"Bioinformatics"},{"key":"2023012711554646300_btu350-B10","doi-asserted-by":"crossref","first-page":"e62732","DOI":"10.1371\/journal.pone.0062732","article-title":"Semi-supervised prediction of SH2-peptide interactions from imbalanced high-throughput data","volume":"8","author":"Kundu","year":"2013","journal-title":"PLoS One"},{"key":"2023012711554646300_btu350-B11","doi-asserted-by":"crossref","first-page":"S5","DOI":"10.1186\/1471-2164-15-S1-S5","article-title":"Cluster based prediction of PDZ-peptide interactions","volume":"15","author":"Kundu","year":"2014","journal-title":"BMC Genomics"},{"key":"2023012711554646300_btu350-B12","doi-asserted-by":"crossref","first-page":"3635","DOI":"10.1093\/nar\/gkg584","article-title":"Scansite 2.0: proteome-wide prediction of cell signaling interactions using short sequence motifs","volume":"31","author":"Obenauer","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"2023012711554646300_btu350-B13","doi-asserted-by":"crossref","first-page":"445","DOI":"10.1126\/science.1083653","article-title":"Assembly of cell regulatory systems through protein interaction domains","volume":"300","author":"Pawson","year":"2003","journal-title":"Science"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/30\/18\/2668\/48929506\/bioinformatics_30_18_2668.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/30\/18\/2668\/48929506\/bioinformatics_30_18_2668.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,27]],"date-time":"2023-01-27T12:41:13Z","timestamp":1674823273000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/30\/18\/2668\/2475615"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,5,28]]},"references-count":13,"journal-issue":{"issue":"18","published-print":{"date-parts":[[2014,9,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btu350","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2014,9,15]]},"published":{"date-parts":[[2014,5,28]]}}}