Interpro

What the Interpro MCP server does

The Interpro MCP server exposes EBI InterPro data through MCP tools. InterPro integrates protein signatures from sources including Pfam, PROSITE, SMART, CDD, and PANTHER. The available data covers protein families, domains, repeats, functional sites, and related classification entries.

The server supports two main research patterns. You can start with a keyword such as a protein function or domain name and identify relevant InterPro accessions. Alternatively, you can start with a UniProt accession and retrieve the InterPro entries assigned to that protein. Entry details can then provide context about what a family or domain represents.

How it works

The hosted service is available at https://gateway.pipeworx.io/interpro/mcp. It uses the gateway’s MCP connection and lists the three InterPro-specific tools alongside shared Pipeworx meta-tools. The gateway can also route broader requests through ask_pipeworx.

For a server containing only the InterPro tools, run the package locally with npx -y @pipeworx/mcp-interpro. The local process communicates over standard input and output and handles MCP initialization, tool discovery, and tool calls. HTTP users can also call tools through the gateway’s REST endpoint, such as POST /v1/tools/search_entries.

Setup and configuration

Add the hosted endpoint to an MCP client as a server URL:

{
  "mcpServers": {
    "interpro": {
      "url": "https://gateway.pipeworx.io/interpro/mcp"
    }
  }
}

For local stdio operation, configure the package command instead:

{
  "mcpServers": {
    "interpro": {
      "command": "npx",
      "args": ["-y", "@pipeworx/mcp-interpro"]
    }
  }
}

No environment variables or API keys are required by the documented setup.

Tools and capabilities

• search_entries searches entry names and accessions by keyword. Results include the InterPro accession, name, type, and member databases.
• get_entry retrieves details for one accession, including its name, type, plain-text description, member-signature and protein counts, and associated GO terms across molecular function, biological process, and cellular component.
• entries_for_protein accepts a UniProt accession and returns matching InterPro families, domains, and sites with their accessions, names, and types.

A typical workflow is to use search_entries to find a candidate entry, pass its accession to get_entry, or use entries_for_protein first when the starting point is a known UniProt protein.

Limitations and notes

The hosted pack endpoint includes shared Pipeworx meta-tools in addition to the InterPro-specific tools, so its tool list is larger than the three tools documented here. The local stdio package exposes only the InterPro tools and does not provide gateway routing through ask_pipeworx.

Results are based on InterPro classifications and the associated UniProt lookup described in the tool documentation.