Pdb Mcp Server

What is Pdb Mcp Server?

A Model Context Protocol (MCP) server that provides programmatic access to the Protein Data Bank (PDB)—the global repository of 3D structures of proteins, nucleic acids, and complex assemblies. It is built for researchers, developers, and bioinformaticians who need to search, retrieve, and analyze macromolecular structures.

How to use Pdb Mcp Server?

Install via npm (npm install && npm build) and configure it as an MCP server in Claude Desktop by adding the built index.js to claude_desktop_config.json. Once configured, you can invoke tools like search_structures, get_structure_info, or download_structure through natural‑language queries, or read resources using URIs such as pdb://structure/{pdb_id}.

Key features of Pdb Mcp Server

• Search PDB by keyword, protein name, or PDB ID
• Retrieve detailed structure information and metadata
• Download coordinates in PDB, mmCIF, mmTF, or XML formats
• Find structures linked to a UniProt accession
• Access validation data and quality metrics

Use cases of Pdb Mcp Server

• Search and browse protein structures for a given keyword (e.g., insulin)
• Obtain full metadata and annotation for a known PDB ID
• Download structure files for downstream analysis or visualization
• Cross‑reference UniProt protein sequences with solved 3D structures
• Inspect structure quality (resolution, R‑free, Ramachandran stats)

FAQ from Pdb Mcp Server

How does this server compare to other protein‑data MCP servers?

It complements the UniProt and AlphaFold MCP servers: this server focuses on experimentally determined structures from PDB, while those servers cover sequence annotations and predicted models respectively.

What are the runtime dependencies?

The server requires Node.js and npm. No external database or API key is needed; it communicates directly with public RCSB PDB APIs.

Where does the data come from?

All data is fetched live from the RCSB Protein Data Bank via their REST, Search, and File Download APIs. No local data is stored by the server.

Are there any known limits or error scenarios?

The server handles invalid PDB IDs, network failures, API rate limiting, missing files, and malformed requests. It does not support user authentication or private data.

What transport protocol does the server use?

The server uses the standard MCP transport (stdio) for local communication with MCP clients like Claude Desktop.