{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,11]],"date-time":"2025-07-11T10:34:33Z","timestamp":1752230073086},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"1","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: cddApp is a Cytoscape extension that supports the annotation of protein networks with information about domains and specific functional sites from the National Center for Biotechnology Information\u2019s conserved domain database (CDD). CDD information is loaded for nodes annotated with NCBI numbers or UniProt identifiers and (optionally) Protein Data Bank structures. cddApp integrates with the Cytoscape apps structureViz2 and enhancedGraphics. Together, these three apps provide powerful tools to annotate nodes with CDD domain and site information and visualize that information in both network and structural contexts.<\/jats:p>\n               <jats:p>Availability and implementation: cddApp is written in Java and freely available for download from the Cytoscape app store ( http:\/\/apps.cytoscape.org ). Documentation is provided at http:\/\/www.rbvi.ucsf.edu\/cytoscape , and the source is publically available from GitHub http:\/\/github.com\/RBVI\/cddApp .<\/jats:p>\n               <jats:p>Contact: \u00a0scooter@cgl.ucsf.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu605","type":"journal-article","created":{"date-parts":[[2014,9,12]],"date-time":"2014-09-12T02:13:15Z","timestamp":1410487995000},"page":"134-136","source":"Crossref","is-referenced-by-count":4,"title":["cddApp: a Cytoscape app for accessing the NCBI conserved domain database"],"prefix":"10.1093","volume":"31","author":[{"given":"John H.","family":"Morris","sequence":"first","affiliation":[{"name":"1 Resource for Biocomputing, Visualization, and Informatics, University of California, San Francisco, CA 94143, USA and 2 National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA"}]},{"given":"Allan","family":"Wu","sequence":"additional","affiliation":[{"name":"1 Resource for Biocomputing, Visualization, and Informatics, University of California, San Francisco, CA 94143, USA and 2 National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA"}]},{"given":"Roxanne A.","family":"Yamashita","sequence":"additional","affiliation":[{"name":"1 Resource for Biocomputing, Visualization, and Informatics, University of California, San Francisco, CA 94143, USA and 2 National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA"}]},{"given":"Aron","family":"Marchler-Bauer","sequence":"additional","affiliation":[{"name":"1 Resource for Biocomputing, Visualization, and Informatics, University of California, San Francisco, CA 94143, USA and 2 National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA"}]},{"given":"Thomas E.","family":"Ferrin","sequence":"additional","affiliation":[{"name":"1 Resource for Biocomputing, Visualization, and Informatics, University of California, San Francisco, CA 94143, USA and 2 National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA"}]}],"member":"286","published-online":{"date-parts":[[2014,9,10]]},"reference":[{"key":"2023020116152202600_btu605-B1","doi-asserted-by":"crossref","first-page":"D521","DOI":"10.1093\/nar\/gkt1130","article-title":"The structure-function linkage database","volume":"42","author":"Akiva","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"2023020116152202600_btu605-B2","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"Altschul","year":"1990","journal-title":"J. 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