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
Installation
cd embl-mcp-server
npm install
npm run buildUsage
{
"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
