InterPro MCP Server

A Model Context Protocol (MCP) server that exposes InterPro to AI clients such as Claude Desktop, Claude Code and claude.ai.

InterPro classifies proteins into families and predicts domains and important functional sites by combining the signatures of its member databases (Pfam, PANTHER, CATH-Gene3D, PROSITE, SMART, CDD, NCBIfam, etc.). This server puts that behind a small set of well-described tools, and coordinates several EMBL-EBI services behind each one so an agent can answer a question with a single call instead of chaining raw REST requests:

  • EBI Search: free-text / keyword discovery when you don’t yet have an accession (“zinc finger”, “kinase domain”).

  • InterPro REST API: authoritative lookups for entries, proteins, structures, domain architectures and taxonomy once an accession is known.

  • InterPro Matches API: precomputed matches for a protein sequence, keyed by its MD5 checksum.

  • InterProScan 6 (Job Dispatcher): runs a full analysis on a novel sequence that isn’t in InterPro yet.

What you can ask

Once the server is connected, you talk to your assistant in plain language and it picks the tools itself. Questions the 13 tools cover:

  • “What is the kringle domain, and which InterPro entry describes it?”

  • “Is the protein kinase domain PF00069 mostly eukaryotic or bacterial?”

  • “What domains are in UniProt P99999, and where are they?”

  • “Which InterPro entries are annotated with GO:0004672?”

  • “Which domain architectures pair a kringle domain with a trypsin domain?”

  • “List reviewed human proteins containing IPR000001.”

  • “What PDB structures contain PF00069?”

  • “Run InterProScan on this sequence and tell me what domains it has.”

See the example workflows and by-tool examples for how each one plays out, and the tool reference for the exact arguments and return shapes.

Connecting

The server is hosted by EMBL-EBI and speaks MCP over Streamable HTTP at https://www.ebi.ac.uk/interpro/mcp. Point your AI client at that URL. Connecting has step-by-step setup for Claude Code, Claude Desktop, claude.ai and other clients. No account or API key is needed.