PDBSAFE

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

1. Get information about a specific structure:

Get detailed information about PDB structure 1ABC using get_structure_info

1. Download structure coordinates:

Download the PDB file for structure 1ABC using download_structure

1. Find structures for a UniProt protein:

Find PDB structures for UniProt accession P01308 using search_by_u