PDB-MCP-Server

PDB-MCP-Server

3.4

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The PDB MCP Server is a Model Context Protocol server that provides access to the Protein Data Bank, offering tools and resources for exploring 3D structures of proteins, nucleic acids, and complex assemblies.

The PDB MCP Server is a specialized server designed to facilitate access to the Protein Data Bank (PDB), the global repository for 3D structural data of biological macromolecules. This server provides a suite of tools and resources that enable researchers, educators, and students to search, retrieve, and analyze structural data of proteins, nucleic acids, and complex assemblies. By leveraging the Model Context Protocol (MCP), the server ensures seamless integration with other MCP-compatible tools and platforms, enhancing the accessibility and usability of PDB data. The server supports various data formats, including PDB, mmCIF, mmTF, and XML, catering to diverse user needs. Additionally, it offers quality metrics and validation data to ensure the reliability of the structural information provided. The PDB MCP Server is an invaluable resource for the scientific community, facilitating advanced research and education in structural biology.

Features

  • Search and retrieve protein structures by keyword, protein name, or PDB ID.
  • Access detailed information and quality metrics for specific PDB structures.
  • Download structure coordinates in multiple formats, including PDB and mmCIF.
  • Find PDB structures associated with UniProt accessions.
  • Integrate with RCSB PDB APIs for comprehensive data access.

Tools

  1. search_structures

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

  2. get_structure_info

    Get detailed information for a specific PDB structure.

  3. download_structure

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

  4. search_by_uniprot

    Find PDB structures associated with a UniProt accession.

  5. get_structure_quality

    Get structure quality metrics and validation data.