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CddApp: a Cytoscape app for accessing the NCBI conserved domain database.

ABSTRACT: 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.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.

SUBMITTER: Morris JH

PROVIDER: S-EPMC4271147 | biostudies-other | 2015 Jan

REPOSITORIES: biostudies-other

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cddApp: a Cytoscape app for accessing the NCBI conserved domain database.

Morris John H JH Wu Allan A Yamashita Roxanne A RA Marchler-Bauer Aron A Ferrin Thomas E TE

Bioinformatics (Oxford, England) 20140910 1

<h4>Motivation</h4>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 po ...[more]

PMID: 25212755

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