cddApp

cddApp annotates protein networks in Cytoscape with conserved domain and functional site information from the National Center for Biotechnology Information's Conserved Domain Database (CDD) to provide domain-level functional context for network analyses.

Key Features:

• CDD domain and site annotation: Loads domain and specific functional site annotations from NCBI's Conserved Domain Database (CDD) onto protein network nodes.
• Identifier support: Maps CDD annotations to nodes using NCBI identifiers and UniProt accession identifiers and can associate annotations with Protein Data Bank (PDB) structures when available.
• Structural mapping: Integrates with structureViz2 to map domain and site annotations onto protein structures for combined network and structural analyses.
• Advanced visualization: Uses enhancedGraphics to render domain and site information within network visualizations and structural contexts.

Scientific Applications:

• Functional annotation of networks: Enriches protein interaction and association networks with conserved domain and functional site information to infer protein function within pathways.
• Structure–function analysis: Supports mapping of conserved sites onto PDB structures to examine the structural context of functional residues and domains.
• Molecular mechanism investigation: Facilitates analysis of domain-level contributions to biological processes and disease-related mechanisms through integrated network and structural data.

Methodology:

Loads CDD domain and functional site data onto network nodes using NCBI or UniProt identifiers, optionally associates annotations with PDB structures via structureViz2, and renders annotations with enhancedGraphics.