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

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

```bash