mcp-rcsb-pdb

RCSB Protein Data Bank experimental structures

Part of Pipeworx — an MCP gateway connecting AI agents to 250+ live data sources.

Tool	Description
`search`	Text search across PDB. Returns matching PDB IDs.
`structure`	Full entry record by PDB ID (e.g. "1abc").
`polymer_entity`	Polymer-entity (chain) metadata.
`ligand`	Non-polymer ligand record (e.g. cofactor, drug).
`assembly`	Biological assembly (defaults to "1" — the first/canonical).
`summary`	Short entry summary.

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 250+ data sources:

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

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.

MIT

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