pdbe-mcp-servers MCP Server

A set of Model Context Protocol (MCP) servers that provides seamless access to the Protein Data Bank in Europe (PDBe) API and PDBe Search. These servers expose PDBe's comprehensive structural…

Local serverstdio

What is the pdbe-mcp-servers MCP Server?

pdbe-mcp-servers is an MCP project maintained in the pdbeurope/pdbe-mcp-servers repository. The maintainer describes its purpose as “A set of Model Context Protocol (MCP) servers that provides seamless access to the Protein Data Bank in Europe (PDBe) API and PDBe Search. These…”. Read the project documentation for the complete scope.

Installation

The documented pypi package is pdbe-mcp-server. The configuration below comes from the maintainer’s example; adapt its paths and account values to your environment.

Source

Project documentation · Repository · Discovery listing. This profile records the public documentation checked on 2026-10-08.

Recorded tools

Check the linked publisher documentation and your connected client's tool list. Names and availability can vary with the server version and account permissions.

Tool	What it does
pdb_id	PDB entry identifier
experimental_method	Structure determination method
release_date	Structure release date
resolution	Structure resolution (Å)
molecule_type	Type of molecule (protein, DNA, RNA, etc.)
organism_scientific_name	Source organism
ligand_name	Bound ligands
title	Structure title/description
get_pdbe_search_schema
run_pdbe_search_query

How to install the pdbe-mcp-servers MCP Server

{
  "mcpServers": {
    "PDBe API Server": {
      "command": "uvx",
      "args": [
        "pdbe-mcp-server",
        "--server-type",
        "pdbe_api_server"
      ]
    }
  }
}

From the project documentation. Replace placeholders and example paths before connecting.