Alphafold

EBI AlphaFold Protein Structure Database MCP — predicted 3-D protein structures for ~214 M sequences. Keyless.

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

Tools

• prediction(qualifier) — full prediction metadata + file URLs (PDB, CIF, PAE)
• summary(qualifier) — short structure summary
• annotations(qualifier, type?) — sequence-level annotations (regions of low pLDDT, etc)
• uniprot(uniprot_id) — same as prediction but explicit UniProt accession

qualifier is a UniProt accession (e.g. P00533).

Data source

https://alphafold.ebi.ac.uk/api/

Quick Start

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

{
  "mcpServers": {
    "alphafold": {
      "url": "https://gateway.pipeworx.io/alphafold/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 Alphafold data" })

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

More

• Docs and guides
• pipeworx.io

License

MIT