PDB MCP Server

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

Installation

Usage

With Claude Desktop

Add to your claude_desktop_config.json:

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

Attribution

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