Pdb MCP Server

🚀 PDB MCP Server

A Model Context Protocol (MCP) server offering access to the Protein Data Bank (PDB), a global repository of information regarding the 3D structures of proteins, nucleic acids, and complex assemblies.

✨ Features

Tools

• search_structures: Search the PDB database for protein structures by keyword, protein name, or PDB ID.
• get_structure_info: Retrieve 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: Obtain 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.

📦 Installation

npm install
npm run build

💻 Usage Examples

With Claude Desktop

Add the following to your claude_desktop_config.json:

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

Example Queries

Basic Usage

# Use the search_structures tool to find insulin protein structures
Use the search_structures tool to find insulin protein structures

Advanced Usage

1. Get information about a specific structure:

# Get detailed information about PDB structure 1ABC using get_structure_info
Get detailed information about PDB structure 1ABC using get_structure_info

2. Download structure coordinates:

# Download the PDB file for structure 1ABC using download_structure
Download the PDB file for structure 1ABC using download_structure

3. Find structures for a UniProt protein:

# Find PDB structures for UniProt accession P01308 using search_by_uniprot
Find PDB structures for UniProt accession P01308 using search_by_uniprot

4. Check structure quality:

# Get validation metrics for PDB structure 1ABC using get_structure_quality
Get validation metrics for PDB structure 1ABC using get_structure_quality

5. Access resources directly:

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

📚 Documentation

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

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

🔧 Technical Details

Development

# Install dependencies
npm install

# Build the server
npm run build

# Run in development mode
npm run dev

📄 License

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:

@misc{pdbmcp2025, 
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}
}