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Updated: Apr 24, 2026

An Integrated Approach for Microprotein Identification and Sequence Analysis
Published on: July 12, 2022
cddApp: a Cytoscape app for accessing the NCBI conserved domain database
John H Morris1, Allan Wu1, Roxanne A Yamashita1
1Resource 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.
cddApp enhances protein network analysis by annotating nodes with conserved domain (CDD) data. This Cytoscape extension integrates with other tools for comprehensive visualization of domain and functional site information.
Area of Science:
- Bioinformatics
- Computational Biology
- Structural Biology
Background:
- Protein networks are crucial for understanding biological processes.
- Annotating these networks with functional information enhances biological insights.
- Existing tools may lack comprehensive integration for domain and site data.
Purpose of the Study:
- To introduce cddApp, a Cytoscape extension for protein network annotation.
- To enable annotation using data from the National Center for Biotechnology Information's Conserved Domain Database (CDD).
- To integrate with existing Cytoscape applications for enhanced visualization.
Main Methods:
- cddApp is a Java-based Cytoscape extension.
- It loads CDD information for nodes with NCBI or UniProt identifiers.
- Integration with structureViz2 and enhancedGraphics apps is supported.
Main Results:
- cddApp facilitates annotation of protein networks with CDD domain and site data.
- It allows visualization of this information within network and structural contexts.
- The extension provides powerful tools for detailed protein network analysis.
Conclusions:
- cddApp offers a valuable tool for researchers analyzing protein networks.
- Integration with other Cytoscape apps provides a comprehensive annotation and visualization solution.
- The freely available nature of cddApp promotes its adoption in the scientific community.
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