*cddApp* is a Cytoscape3 extension that supports the annotation of protein networks with information about domains and specific functional sites (features) from the National Center for Biotechnology Information (NCBI) Conserved Domain Database (CDD). CDD information is loaded for nodes annotated with GI numbers or UniProt Identifiers and (optionally) PDB structures. *cddApp* integrates with the Cytoscape apps [http://apps.cytoscape.org/apps/structureViz2 *structureViz2*] and [http://apps.cytoscape.org/apps/enhancedGraphics 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.
