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Research & Data · Education & Learning

Pdb MCP Server

augmented-nature/pdb-mcp-server

A Model Context Protocol (MCP) server that provides access to the Protein Data Bank (PDB) - the worldwide repository of information about the 3D structures of proteins, nucleic acids, and complex assemblies.

View on GitHub

Install

Client configuration

{
  "mcpServers": {
    "pdb-server": {
      "command": "node",
      "args": [
        "/path/to/pdb-server/build/index.js"
      ]
    }
  }
}
Author
@augmented-nature
Category
Research & Data, Education & Learning
Updated
Oct 6, 2026

Features

  • pdb://structure/{pdb_id}: Complete structure information for a PDB ID

  • pdb://coordinates/{pdb_id}: Structure coordinates in PDB format

  • pdb://mmcif/{pdb_id}: Structure data in mmCIF format

  • pdb://validation/{pdb_id}: Structure validation data and quality metrics

  • pdb://ligands/{pdb_id}: Ligand and binding site information

Tools (5)

  • search_structures

    Search PDB database for protein structures by keyword, protein name, or PDB ID

  • get_structure_info

    Get detailed information for a specific PDB structure

  • download_structure

    Download structure coordinates in various formats (PDB, mmCIF, mmTF, XML)

  • search_by_uniprot

    Find PDB structures associated with a UniProt accession

  • get_structure_quality

    Get structure quality metrics and validation data

Details on this page are taken from the project's README. Open README

Supported clients

Clients mentioned in this server's README:

View all
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