mcp-rcsb-pdb

RCSB Protein Data Bank experimental structures

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

Tools

| 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. |

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 250+ 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

• All tools and guides
• pipeworx.io

License

MIT