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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

License

MIT

A
license - permissive license
-
quality - not tested
C
maintenance

Resources

Unclaimed servers have limited discoverability.

Looking for Admin?

If you are the server author, to access and configure the admin panel.

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MCP directory API

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curl -X GET 'https://glama.ai/api/mcp/v1/servers/pipeworx-io/mcp-rcsb-pdb'

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