PDB-MCP-Server

Overview

The PDB-MCP-Server is a specialized MCP server that provides programmatic access to the Protein Data Bank (PDB), which contains 3D structural information about proteins, nucleic acids, and complex assemblies. It offers both tools and resources for accessing structural data, with capabilities ranging from keyword searches to detailed structure retrieval and quality metrics. The server integrates with RCSB PDB APIs to provide comprehensive structural biology information.

Try asking AI

After installing, here are 5 things you can ask your AI assistant:

• search_structures

  Search PDB database for protein structures by keyword, protein name, or PDB ID

  Try:Search for insulin structuresTry:Find PDB entries for hemoglobin
• get_structure_info

  Get detailed information for a specific PDB structure

  Try:Get detailed information about PDB structure 1ABCTry:Tell me about structure 4HHB
• download_structure

  Download structure coordinates in various formats (PDB, mmCIF, mmTF, XML)

  Try:Download the PDB file for structure 1ABCTry:Get structure 2VIU in mmCIF format
• search_by_uniprot

  Find PDB structures associated with a UniProt accession

  Try:Find PDB structures for UniProt accession P01308Try:Show structures for UniProt ID P00533
• get_structure_quality

  Get structure quality metrics and validation data

  Try:Get validation metrics for PDB structure 1ABCTry:Check quality of structure 3TGL

Comparable tools

Installation

npm install
npm run build

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

FAQ

What data formats does this server provide?

The server provides structure coordinates in PDB, mmCIF, mmTF, and XML formats, along with validation data and quality metrics.

Can I search structures by UniProt accession?

Yes, the server includes a search_by_uniprot tool to find PDB structures associated with specific UniProt accessions.

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