mcp-complex-portal

EBI Complex Portal MCP.

Part of Pipeworx — an MCP gateway connecting AI agents to 1394+ live data sources.

Tools

Tool	Description
search_complexes	Search the EBI Complex Portal — a manually curated database of stable macromolecular protein complexes — by protein/complex name, gene, GO term, or biological process (e.g. "apoptosis", "SCF", "ribosome"). Returns matching complexes with their accession (e.g. CPX-7762), name, description, and organism. Keyless. Complements UniProt/IntAct/STRING.
get_complex	Get a single Complex Portal record by its accession (e.g. CPX-7762). Returns the complex's participants (subunits) with UniProt identifiers, biological roles and stoichiometry, plus systematic name, function, species, and description. Keyless. Complements UniProt/IntAct/STRING.

Quick Start

Add to your MCP client (Claude Desktop, Cursor, Windsurf, etc.):

{
  "mcpServers": {
    "complex-portal": {
      "url": "https://gateway.pipeworx.io/complex-portal/mcp"
    }
  }
}

Or connect to the full Pipeworx gateway for access to all 1394+ data sources:

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

Using with ask_pipeworx

Instead of calling tools directly, you can ask questions in plain English:

ask_pipeworx({ question: "your question about Complex Portal data" })

The gateway picks the right tool and fills the arguments automatically.

More

• Docs and guides
• pipeworx.io

License

MIT