cddApp: a Cytoscape app for accessing the NCBI conserved domain database.
other · Level V
Where this comes from
- Record sourced from PubMed, PMID 25212755.
- Also identified by DOI 10.1093/bioinformatics/btu605 and PMC identifier 4271147.
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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.
Medical subject headings
- Bacterial Proteins
- Computational Biology
- Metabolic Networks and Pathways
- Molecular Sequence Annotation
- Sequence Analysis, Protein
- Software