Alphafold

AlphaFold DB MCP — predicted protein structures.

Part of Pipeworx — an MCP gateway connecting AI agents to 965+ live data sources.

Tools

Tool	Description
prediction	Full prediction metadata + structure file URLs (PDB, CIF, PAE).
summary	Short summary for a prediction (organism, sequence, mean pLDDT).
annotations	Sequence-level annotations (e.g. MUTAGEN, LOW_CONFIDENCE_REGIONS).
uniprot	Fetch AlphaFold structure prediction metadata (PDB/CIF/PAE download URLs, pLDDT scores) by UniProt accession (e.g. "P00533"); equivalent to prediction but takes uniprot_id explicitly.

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 965+ 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

• All tools and guides
• pipeworx.io

License

MIT