Gene3D structural

Gene3D structural annotates protein sequences to provide structural and functional annotations by scanning against the CATH profile-HMM library and integrating annotations from UniProt, RefSeq, Integr8, CATH, PFAM, and DRUGBANK to characterize protein families.

Key Features:

• Structural annotation via CATH: Protein sequences are scanned against the CATH profile-HMM library, which is based on manually curated structural domains from the Protein Data Bank (PDB) and organized into a hierarchy reflecting topology, homology, and conservation, enabling inference of ancient and divergent homology relationships.
• Pfam and supplementary predictions: Incorporates Pfam-A family annotations, coiled-coil predictions, and experimental annotations from UniProt.
• Integration of authoritative databases: Aggregates annotations and cross-references from UniProt, RefSeq, Integr8, CATH, PFAM, and DRUGBANK.
• Functional and interaction annotations: Amalgamates protein-protein interaction data, Gene Ontology (GO) functional assignments, KEGG pathways, FUNCAT descriptions, and links to microarray expression data.
• Database coverage: Contains over 3.5 million domain assignments for nearly 5 million proteins encompassing data from 527 completed genomes.

Scientific Applications:

• Evolutionary and structural inference: Identification of distant homology and structural domain relationships to support evolutionary analyses.
• Functional genomics: Assignment of GO terms, FUNCAT descriptions, and Pfam families to support gene function prediction and annotation.
• Pathway and systems biology analysis: Integration with KEGG and protein-protein interaction data to facilitate pathway mapping and network studies.
• Drug discovery support: Cross-references to DRUGBANK and structural domain annotations to inform target characterization.
• Expression and disease mechanism studies: Links to microarray expression data and integrated annotations to support investigations of expression profiles and disease-related processes.

Methodology:

Protein sequences are scanned against the CATH profile-HMM library; Pfam-A annotations, coiled-coil predictions, UniProt experimental data, protein-protein interaction data, Gene Ontology, KEGG, FUNCAT, and microarray links are integrated.