EMBL-EBI MCP Server

Model Context Protocol (MCP) server for EMBL-EBI bioinformatics APIs — InterPro protein domains, Pfam families, protein sequence features, and taxonomy.

Features

• Single unified tool (embl_data) with 6 methods

• No API key required — uses public EMBL-EBI APIs

• InterPro domain/family search and lookup

• Pfam protein family search

• Protein sequence feature annotation (domains, sites, regions)

• NCBI taxonomy search

Related MCP server: Ensembl MCP Server

Installation

cd embl-mcp-server
npm install
npm run build

Usage

{
  "mcpServers": {
    "embl": {
      "command": "node",
      "args": ["/path/to/embl-mcp-server/build/index.js"]
    }
  }
}

Tool: embl_data

Single unified tool with multiple methods accessed via the method parameter.

Methods

1. search_interpro

Search InterPro protein families and domains.

{
  "method": "search_interpro",
  "query": "kinase",
  "limit": 10
}

Returns: accession, name, type (family/domain/repeat), description.

2. get_interpro_entry

Get full InterPro entry details.

{
  "method": "get_interpro_entry",
  "accession": "IPR000719"
}

Returns: name, type, description, GO terms, literature references.

3. get_protein_domains

Get all InterPro domains mapped to a UniProt protein.

{
  "method": "get_protein_domains",
  "uniprot_id": "P04637"
}

Returns: domain entries with positions on the protein sequence.

4. search_pfam

Search Pfam protein families.

{
  "method": "search_pfam",
  "query": "SH2 domain",
  "limit": 10
}

Returns: Pfam accession, name, type, description.

5. get_protein_features

Get all sequence features for a UniProt protein.

{
  "method": "get_protein_features",
  "uniprot_id": "P04637"
}

Returns: features array with type, description, location (begin/end), evidence.

6. search_taxonomy

Search NCBI taxonomy via EBI.

{
  "method": "search_taxonomy",
  "query": "homo sapiens",
  "limit": 5
}

Returns: taxId, scientificName, displayName.

Data Source

• InterPro: https://www.ebi.ac.uk/interpro/api — 47,000+ protein families/domains

• Proteins API: https://www.ebi.ac.uk/proteins/api — sequence features

• ENA Taxonomy: https://www.ebi.ac.uk/ena/taxonomy — NCBI taxonomy

• Rate limits: No hard limits

License

MIT