title: cddApp: a Cytoscape app for accessing the NCBI conserved domain database.
abstract: BACKGROUND
  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's 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.
  
  
  METHODS
  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.
authors.affiliation: Resource for Biocomputing, Visualization, and Informatics, University of California, San Francisco, CA 94143, USA and National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
authors.forename: John H
authors.initials: JH
authors.lastname: Morris
authors.affiliation: Resource for Biocomputing, Visualization, and Informatics, University of California, San Francisco, CA 94143, USA and National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
authors.forename: Allan
authors.initials: A
authors.lastname: Wu
authors.affiliation: Resource for Biocomputing, Visualization, and Informatics, University of California, San Francisco, CA 94143, USA and National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
authors.forename: Roxanne A
authors.initials: RA
authors.lastname: Yamashita
authors.affiliation: Resource for Biocomputing, Visualization, and Informatics, University of California, San Francisco, CA 94143, USA and National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
authors.forename: Aron
authors.initials: A
authors.lastname: Marchler-Bauer
authors.affiliation: Resource for Biocomputing, Visualization, and Informatics, University of California, San Francisco, CA 94143, USA and National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
authors.forename: Thomas E
authors.initials: TE
authors.lastname: Ferrin
mesh_terms: D000465:Algorithms; D001407:Bacillus; D001426:Bacterial Proteins / Q000737:chemistry / Q000378:metabolism*; D019295:Computational Biology / Q000295:instrumentation*; D017124:Conserved Sequence; D030562:Databases, Protein; D006801:Humans; D053858:Metabolic Networks and Pathways; D058977:Molecular Sequence Annotation / Q000379:methods*; D011487:Protein Conformation; D025941:Protein Interaction Mapping; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software
chemical_list: D001426:Bacterial Proteins