lamm-mit InterPro Database Skill Documentation
Overview
InterPro is a comprehensive protein annotation resource maintained by EMBL-EBI that integrates signatures from 13 member databases. It classifies proteins into families, domains, homologous superfamilies, repeats, and functional sites, covering over 100 million protein sequences.
Primary Use Cases
- Predicting functions of uncharacterized proteins
- Analyzing domain architecture and composition
- Classifying proteins into evolutionary families
- Mapping Gene Ontology terms to sequences
- Conducting evolutionary and structural analyses
Core API Functions
Protein Lookup: Query InterPro entries for any UniProt identifier using the /protein/UniProt/{id}/entry/InterPro/ endpoint.
Entry Details: Retrieve comprehensive information about specific InterPro entries through /entry/InterPro/{id}/ or member database-specific endpoints.
Reverse Lookup: "Get all proteins annotated with an InterPro entry" via /entry/InterPro/{id}/protein/UniProt/ to discover related sequences.
Domain Architecture: Obtain complete positional mapping of domains across a protein sequence.
GO Term Mapping: Extract Gene Ontology annotations embedded within InterPro entry metadata.
Integration Strategy
- Utilize UniProt accession numbers for reliable queries
- Distinguish between broad family classifications and specific structural domains
- Implement rate limiting (0.3 seconds between requests) for batch operations
- Combine results with UniProt and PDB data for enriched biological context
Technical Implementation
All queries use the REST API at https://www.ebi.ac.uk/interpro/api/ with JSON responses. Python implementations employ the requests library with appropriate headers and error handling.