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EBI InterPro

EBI InterPro MCP Connector for Claude

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Classify protein sequences into families, predict functional domains, and explore evolutionary relationships across species.

16 tools Official Updated Jun 28, 2026 Official Vinkius Partner
More Details Connect to Claude

Connect to the InterPro API and access the world's most comprehensive resource for protein family, domain, and functional site classification.

What you can do

  • Domain Classification — Retrieve detailed InterPro entry information including family/domain descriptions, GO terms, and member database cross-references
  • Multi-Database Access — Query entries from Pfam, CDD, SMART, Prosite, PANTHER, Gene3D, HAMAP, and more through a unified interface
  • Protein Annotation — Find all InterPro domains, families, and sites annotated on any UniProt protein
  • Structure Mapping — Discover PDB structures containing proteins that match specific InterPro entries
  • Taxonomic Distribution — Explore which organisms contain proteins matching a domain or family — essential for evolutionary biology
  • Proteome Coverage — Assess domain annotation coverage for complete proteomes
  • Clan Analysis — Navigate Pfam clan hierarchies to understand super-family relationships

How it works

  1. Subscribe to this server
  2. No API key required — the InterPro API is fully public
  3. Start classifying proteins from Claude, Cursor, or any MCP-compatible client

Your AI agent becomes a protein domain expert with access to InterPro's unified classification of protein families from 13+ member databases. All data is sourced from the official InterPro REST API maintained by EMBL-EBI.

Who is this for?

  • Molecular Biologists — classify unknown proteins into families and predict their functional domains
  • Evolutionary Biologists — explore taxonomic distributions of protein domains across the tree of life
  • Structural Biologists — find 3D structures containing specific protein domains for comparative analysis
  • Bioinformaticians — integrate protein family classifications into automated annotation pipelines
interpropfamprotein-domainsprotein-familiesbioinformaticsembl-ebifunctional-annotation

16 tools expose this connector's capabilities to your AI agent.

get_cdd_entry

CDD provides curated models for protein domain families and includes additional alignment and structure data. Use accessions like cd00001. Get CDD (Conserved Domain Database) entry details

get_clan

Returns clan accession, name, description, and member counts. Use Pfam clan accessions like CL0001. Get Pfam clan (super-family grouping) details

get_entry

Returns name, type (family, domain, homologous superfamily, repeat, site), description, Gene Ontology terms, member database cross-references, and literature count. Use accessions like IPR000001, IPR036291. Get InterPro entry metadata for a family or domain

get_entry_proteins

Returns protein accessions, names, lengths, and source organisms. Useful for finding all members of a protein family across the UniProt database. Get all proteins matching an InterPro entry

get_entry_structures

Returns PDB IDs, names, experiment types, and resolutions. Useful for finding structural representatives of a protein family or domain. Get all PDB structures matching an InterPro entry

get_entry_taxonomy

Returns taxonomy nodes with names, ranks, and protein counts. This answers the evolutionary biology question "which organisms have this domain/family?" and is essential for understanding protein evolution and conservation. Get taxonomic distribution of an InterPro entry

get_pfam_entry

Pfam is the most widely used protein domain database. Use accessions like PF00069 (kinase domain), PF00076 (RRM domain). Get Pfam domain or family details

get_protein

Returns the protein name, length, source organism, evidence level, fragment status, and counters for how many InterPro entries, Pfam domains, structures, and taxa are associated with it. Get protein details with all domain and family assignments

get_protein_entries

This is the key tool for understanding "what domains does my protein have?" — the fundamental question in protein characterization. Get all InterPro entries matching a specific protein

get_proteome

Returns proteome ID, organism name, strain, reference status, and counters for associated entries and proteins. Use UniProt proteome IDs like UP000005640 (human). Get proteome details with domain coverage statistics

get_structure

Use a 4-character PDB ID like 1cbs or 4hhb. Get a PDB structure with mapped InterPro annotations

get_taxonomy

Returns the organism name, rank, lineage, number of children taxa, and counters for associated InterPro entries and proteins. Use IDs like 9606 (human), 10090 (mouse), 562 (E. coli). Get taxonomic node with entry and protein counts

list_entry_databases

Shows the number of entries in each database. Useful for understanding the scope of available domain and family annotations. List all InterPro member databases and entry counts

search_entries

Optionally filter by entry type: family, domain, homologous_superfamily, repeat, or site. Returns accessions, names, types, and protein/structure counts. Use queries like "kinase", "zinc finger", "immunoglobulin". Search InterPro entries by keyword and type

search_proteins

Returns UniProt accessions, names, lengths, organisms, and annotation counts. Use queries like "insulin", "hemoglobin", "BRCA1". Search proteins in InterPro by name or keyword

search_taxonomy

Returns taxon IDs, names, ranks, and annotation counts. Use queries like "human", "drosophila", "arabidopsis", "saccharomyces". Search taxonomy by organism name

See how to talk to your AI agent using EBI InterPro.

What domains and families does the human TP53 protein belong to?

I've retrieved all InterPro annotations for TP53 (P04637). The protein is classified into the p53 tumor suppressor family (IPR002117), contains a p53 DNA-binding domain (IPR011615), a p53 tetramerization domain (IPR010991), and a transactivation domain. These domains are conserved across vertebrates and define the functional architecture of p53 as a transcription factor and tumor suppressor.

Show me all member databases in InterPro and how many entries each has.

I've retrieved the InterPro database overview. The platform integrates 13+ member databases: Pfam leads with over 20,000 families and domains, followed by PANTHER, Gene3D, and CDD with thousands of entries each. SMART, Prosite, HAMAP, PRINTS, PIRSF, SFLD, NCBIfam, and AntiFam complete the collection. InterPro itself has over 46,000 integrated entries that unify signatures across these databases.

Which organisms have the kinase domain PF00069?

I found the Pfam entry PF00069 (protein kinase domain) and retrieved its InterPro integration (IPR000719). The taxonomic distribution shows this domain is universally conserved across all kingdoms of life — from bacteria and archaea to plants, fungi, and animals. The human genome alone contains hundreds of kinase domain-containing proteins, making this one of the most expanded protein families in eukaryotic evolution.

No. The InterPro API is completely public and requires no authentication. Enter any placeholder value in the API key field to activate the server immediately.

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