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.

Features

Tools

• 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

Resources

• 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

• pdb://search/{query}: Search results for structures matching the query

Related MCP server: DevDb MCP Server

Installation

npm install
npm run build

Usage

With Claude Desktop

Add to your claude_desktop_config.json:

{
  "mcpServers": {
    "pdb-server": {
      "command": "node",
      "args": ["/path/to/pdb-server/build/index.js"]
    }
  }
}

Example Queries

1. Search for insulin structures:

   Use the search_structures tool to find insulin protein structures

2. Get information about a specific structure:

   Get detailed information about PDB structure 1ABC using get_structure_info

3. Download structure coordinates:

   Download the PDB file for structure 1ABC using download_structure

4. Find structures for a UniProt protein:

   Find PDB structures for UniProt accession P01308 using search_by_uniprot

5. Check structure quality:

   Get validation metrics for PDB structure 1ABC using get_structure_quality

6. Access resources directly:

   Show me the resource pdb://structure/1abc

API Integration

This server integrates with:

• RCSB PDB REST API (https://data.rcsb.org/): For structure metadata and information

• RCSB PDB Search API (https://search.rcsb.org/): For advanced search capabilities

• RCSB PDB File Download (https://files.rcsb.org/): For structure file downloads

Structure Data Formats

• PDB: Original Protein Data Bank format

• mmCIF: Macromolecular Crystallographic Information File (newer standard)

• mmTF: Macromolecular Transmission Format (binary, compressed)

• XML: Extensible Markup Language format

Quality Metrics

The server provides various structure quality indicators:

• Resolution (for X-ray crystallography)

• R-work and R-free values

• Ramachandran plot statistics

• Clash scores

• Rotamer outliers

• Model validation scores

Complementary Servers

This PDB server works well with:

• UniProt MCP Server: For protein sequence and functional information

• AlphaFold MCP Server: For predicted protein structures

Together, these provide comprehensive access to protein structure and function data.

Error Handling

The server includes robust error handling for:

• Invalid PDB IDs

• Network connectivity issues

• API rate limiting

• Missing structure files

• Malformed requests

Development

# Install dependencies
npm install

# Build the server
npm run build

# Run in development mode
npm run dev

Attribution

This project is developed by Augmented Nature 🌐 Website: augmentednature.ai

Citation

If you use this project in your research or publications, please cite it as follows:

author = {Moudather Chelbi},
title = {Protein Data Bank (PDB) MCP Server},
year = {2025},
howpublished = {https://github.com/Augmented-Nature/PDB-MCP-Server},
note = {Accessed: 2025-06-29}