{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,3,25]],"date-time":"2024-03-25T07:32:11Z","timestamp":1711351931116},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"19","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2008,10,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: \u00a0Cytoprophet is a software tool that allows prediction and visualization of protein and domain interaction networks. It is implemented as a plug-in of Cytoscape, an open source software framework for analysis and visualization of molecular networks. Cytoprophet implements three algorithms that predict new potential physical interactions using the domain composition of proteins and experimental assays. The algorithms for protein and domain interaction inference include maximum likelihood estimation (MLE) using expectation maximization (EM); the set cover approach maximum specificity set cover (MSSC) and the sum-product algorithm (SPA). After accepting an input set of proteins with Uniprot ID\/Accession numbers and a selected prediction algorithm, Cytoprophet draws a network of potential interactions with probability scores and GO distances as edge attributes. A network of domain interactions between the domains of the initial protein list can also be generated. Cytoprophet was designed to take advantage of the visual capabilities of Cytoscape and be simple to use. An example of inference in a signaling network of myxobacterium Myxococcus xanthus is presented and available at Cytoprophet's website.<\/jats:p>\n               <jats:p>Availability: \u00a0http:\/\/cytoprophet.cse.nd.edu<\/jats:p>\n               <jats:p>Contact: \u00a0cytoprophet@cse.nd.edu<\/jats:p>\n               <jats:p>Supplementary information: Examples and supplementary data are accessible at http:\/\/cytoprophet.cse.nd.edu<\/jats:p>","DOI":"10.1093\/bioinformatics\/btn380","type":"journal-article","created":{"date-parts":[[2008,7,25]],"date-time":"2008-07-25T00:14:32Z","timestamp":1216944872000},"page":"2265-2266","source":"Crossref","is-referenced-by-count":10,"title":["Cytoprophet: a <i>Cytoscape<\/i> plug-in for protein and domain interaction networks inference"],"prefix":"10.1093","volume":"24","author":[{"given":"Faruck","family":"Morcos","sequence":"first","affiliation":[{"name":"1 Department of Computer Science and Engineering and 2Department of Electrical Engineering, University of Notre Dame, Notre Dame, IN 46556, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Charles","family":"Lamanna","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science and Engineering and 2Department of Electrical Engineering, University of Notre Dame, Notre Dame, IN 46556, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marcin","family":"Sikora","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science and Engineering and 2Department of Electrical Engineering, University of Notre Dame, Notre Dame, IN 46556, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jes\u00fas","family":"Izaguirre","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science and Engineering and 2Department of Electrical Engineering, University of Notre Dame, Notre Dame, IN 46556, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2008,7,24]]},"reference":[{"issue":"Database issue","key":"2023020211251314200_B1","doi-asserted-by":"crossref","first-page":"D138","DOI":"10.1093\/nar\/gkh121","article-title":"The pfam protein families database","volume":"32","author":"Bateman","year":"2004","journal-title":"Nucleic Acids Res"},{"issue":"Database issue","key":"2023020211251314200_B2","doi-asserted-by":"crossref","first-page":"D193","DOI":"10.1093\/nar\/gkl929","article-title":"The universal protein resource (uniprot)","volume":"35","author":"Consortium","year":"2007","journal-title":"Nucleic Acids Res"},{"key":"2023020211251314200_B3","doi-asserted-by":"crossref","first-page":"1540","DOI":"10.1101\/gr.153002","article-title":"Inferring domain-domain interactions from protein-protein interactions","volume":"12","author":"Deng","year":"2002","journal-title":"Genome Res"},{"issue":"Database issue","key":"2023020211251314200_B4","doi-asserted-by":"crossref","first-page":"D233","DOI":"10.1093\/nar\/gki057","article-title":"The rcsb protein data bank: a redesigned query system and relational database based on the mmcif schema","volume":"33","author":"Deshpande","year":"2005","journal-title":"Nucleic Acids Res"},{"key":"2023020211251314200_B5","doi-asserted-by":"crossref","first-page":"78","DOI":"10.1109\/TCBB.2007.1001","article-title":"Predicting protein-protein interactions form protein domains using a set cover approach","volume":"4","author":"Huang","year":"2007","journal-title":"IEEE\/ACM Trans. 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