PDBe-MCP-Servers

Name: PDBe-MCP-Servers
Availability: InStock
Author: PDBe EMBL-EBI

PDBe MCP Servers integrate Protein Data Bank Europe resources with LLMs via Model Context Protocol. Provides seamless access to protein structure data through API tools and graph database schema assistance for intelligent Cypher query generation, bridging structural biology and AI research.

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README

PDBe MCP Servers

A set of Model Context Protocol (MCP) servers that provides seamless access to the Protein Data Bank in Europe (PDBe) API and PDBe Graph Database. This server exposes PDBe's comprehensive structural biology data as MCP tools, enabling direct integration with Claude Desktop and other AI-powered applications.

Prerequisites

Python 3.10+ - Required for the server runtime
uv - Fast Python package manager and dependency resolver

Installation

Quick Start

Clone and navigate to the repository:

git clone https://github.com/PDBeurope/PDBe-MCP-Servers.git
cd PDBe-MCP-Servers

Create a virtual environment:
```
uv venv
```
Install with uv:
```
uv pip install .
```

Claude Desktop Integration

Configuration

Locate your Claude Desktop configuration file:
- macOS: ~/Library/Application Support/Claude/claude_desktop_config.json
- Windows: %APPDATA%\Claude\claude_desktop_config.json
- Linux: ~/.config/Claude/claude_desktop_config.json

Add the PDBe MCP server configuration:

{
  "mcpServers": {
    "PDBe API": {
      "command": "/usr/local/bin/uv",
      "args": [
        "run",
        "--directory",
        "/path/to/your/PDBe-MCP-Servers",
        "pdbe-mcp-server",
        "--server-type",
        "pdbe_api_server"
      ]
    },
    "PDBe Graph": {
      "command": "/usr/local/bin/uv",
      "args": [
        "run",
        "--directory",
        "/path/to/your/PDBe-MCP-Servers",
        "pdbe-mcp-server",
        "--server-type",
        "pdbe_graph_server"
      ]
    }
  }
}

Note: Before proceeding, ensure that uv is installed and available in your system's PATH. If uv is installed in a non-standard location, update the path accordingly by using which uv. Also, double-check that the /path/to/your/PDBe-MCP-Servers in the configuration matches the actual directory where you cloned the repository.

Restart Claude Desktop to load the new configuration.

Using in Claude

Once configured, you can access PDBe tools directly in your Claude conversations:

Search for protein structures: "Find structures for UniProt accession P12345"
Explore molecular interactions: "Show me ligand binding sites for this protein"

The tools will appear in Claude's "Search and tools" interface, where you can enable or disable them as needed.

Server Types

pdbe_api_server: Core PDBe REST API access with essential structural data
pdbe_graph_server: Know more about the PDBe Graph Database and generate Cypher queries for accessing complex relationships and interactions.

Development and Advanced Usage

Development Installation

For contributing or development work:

uv pip install -e ".[dev]"

Node.js (optional) - For using the MCP Inspector development tool

Starting the Server Manually

Choose between two server types based on your needs:

PDBe API Server

Provides access to core PDBe REST API endpoints:

uv run pdbe-mcp-server --server-type pdbe_api_server --transport sse

PDBe Graph Database Server

Enables complex relationship queries and network analysis:

uv run pdbe-mcp-server --server-type pdbe_graph_server --transport sse

The server will start at http://localhost:8000/sse by default.

Development and Testing

Explore available tools and test API responses:

npx @modelcontextprotocol/inspector

The MCP Inspector provides an interactive interface to browse tools, test queries, and validate responses before integrating with your application.

Server Configuration

Transport Options

stdio: Default mode - Optimal for direct client integration like Claude Desktop
SSE (Server-Sent Events): --transport sse - Best for web-based clients and development