@pipeworx/rcsb-pdb

RCSB Protein Data Bank MCP — 3-D structure metadata for ~225 k experimentally determined macromolecules. Keyless.

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

Tools

• search(query, return_type?, limit?) — text search across PDB

• structure(pdb_id) — full entry record (experiment, ligands, polymer entities)

• polymer_entity(pdb_id, entity_id) — single polymer entity (chain) metadata

• ligand(pdb_id, ligand_id) — ligand record

• assembly(pdb_id, assembly_id?) — biological assembly

• summary(pdb_id) — short summary view

Related MCP server: Structural Biology MCP Server

Data sources

• Search: https://search.rcsb.org/rcsbsearch/v2/query

• Data: https://data.rcsb.org/rest/v1/core/

Quick Start

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

{
  "mcpServers": {
    "rcsb-pdb": {
      "url": "https://gateway.pipeworx.io/rcsb-pdb/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 Rcsb Pdb data" })

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

More

• Docs and guides

• pipeworx.io

License

MIT