Gene3D

Gene3D provides structural domain annotations for proteins by mapping sequences to CATH-derived domain superfamilies and integrating these annotations with functional, genomic, and molecular data.

Key Features:

• Gene3DScan: Identifies structural domains within protein sequences.
• Pre-calculated Annotations: Provides pre-computed domain annotations for major sequence databases.
• Linked Functional Annotation: Integrates functional annotations from UniProt, Gene Ontology (GO), KEGG, and EC numbers with structural domain data.
• Programmatic Web Services: Exposes CATH-Gene3D annotation resources via HTTP web services with multiple output formats.
• CATH-derived Coverage: Annotates over 7 million proteins using manually curated structural domain superfamilies from the CATH database.
• External Resource Integration: Links domain annotations to genomic and taxonomic information via the NCBI Taxonomy database.

Scientific Applications:

• GO term retrieval: Retrieve curated Gene Ontology (GO) terms associated with specific domain superfamilies.
• Multi-domain architecture analysis: Analyze multi-domain architectures within the human genome or other organisms.
• Pipeline integration: Incorporate domain annotations into locally run pipelines and analysis software.

Methodology:

Integrates manually curated structural domain superfamilies from CATH with external resources including Gene Ontology (GO), EC numbers, UniProt, and the NCBI Taxonomy database; Gene3DScan identifies structural domains in protein sequences and CATH-Gene3D annotations are exposed via programmatic HTTP web services.