pdbe-mcp-server 1.0.6

A Model Context Protocol (MCP) server for accessing PDBe (Protein Data Bank in Europe) structural biology data and services

PDBe MCP Servers

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

Features:

• PDBe API Server: Access core structural data through REST API endpoints
• PDBe Graph Server: Query complex relationships and molecular interactions
• PDBe Search Server: Perform advanced Solr-based searches across structural data

Prerequisites

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

Installation

Quick Start

Install directly from PyPI:

uvx pdbe-mcp-server

The tool is available on PyPI and can be run directly with uvx without any installation step.

Alternative: Local Development Installation

For development work or customization:

1. Clone and navigate to the repository:

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

2. Create a virtual environment:

   uv venv
   

3. Install with uv:

   uv pip install .
   

Claude Desktop Integration

Configuration

1. 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

2. Add the PDBe MCP server configuration:

   For PyPI installation (recommended):

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

   For local development installation:

   {
     "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"
         ]
       },
       "PDBe Search": {
         "command": "/usr/local/bin/uv",
         "args": [
           "run",
           "--directory",
           "/path/to/your/PDBe-MCP-Servers",
           "pdbe-mcp-server",
           "--server-type",
           "pdbe_search_server"
         ]
       }
     }
   }
   

Note:

• For the PyPI installation method, ensure uvx is available in your PATH (this comes with uv)
• For local development, ensure that uv is installed and the /path/to/your/PDBe-MCP-Servers matches your actual directory

3. 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"
• Query structure releases: "Show me all structures released this month grouped by experimental method"
• Explore molecular interactions: "Show me ligand binding sites for this protein"
• Advanced search queries: "Find all X-ray crystal structures with resolution better than 2.0 Å from 2024"

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
• pdbe_search_server: Advanced Solr-based search capabilities for complex structural queries and data analysis

Search Server Features

The PDBe Search Server provides powerful querying capabilities through the PDBe Solr search interface:

Available Tools

pdbe_graph_nodes

Retrieves metadata about all node types (labels) defined in the PDBe graph database schema. Use this to understand the different types of entities and their properties.

Example usage:

"Show me all node types in the PDBe graph database"

pdbe_graph_edges

Retrieves metadata about all relationship types (edges) defined in the PDBe graph database schema. Use this to understand how entities are connected.

Example usage:

"Show me all relationship types in the PDBe graph database"

pdbe_graph_example_queries

Retrieves example Cypher queries that demonstrate how to interact with the PDBe graph database.

Example usage:

"Give me example Cypher queries for exploring the PDBe graph"

pdbe_run_cypher_query

Execute custom read-only Cypher queries against a Neo4j graph database. Only available when Neo4j environment variables are configured.

Parameters:

• cypher_query (required): The Cypher query to execute. Only MATCH and OPTIONAL MATCH queries are allowed.

Example usage:

"Execute query: MATCH (s:Structure) WHERE s.PDB_ID = '1abc' RETURN s.TITLE as title"
"Find ligands: MATCH (s:Structure)-[:HAS_LIGAND]->(l:Ligand) WHERE s.PDB_ID = '1abc' RETURN l.name"

Note: Write operations (MERGE, CREATE, DELETE, REMOVE, SET, LOAD CSV, FOREACH) are blocked for safety.

get_search_schema

Retrieves the complete Solr search schema showing all available fields, data types, and descriptions. Use this to understand what fields you can search and filter on.

Example usage:

"Show me the search schema for PDBe structures"

run_search_query

Execute advanced search queries with flexible filtering, sorting, and pagination options.

Parameters:

• query (required): Solr query string (e.g., pdb_id:1cbs, experimental_method:"X-ray diffraction")
• filters (optional): Array of field names to include in results
• sort (optional): Sort criteria (e.g., release_date desc, resolution asc)
• start (optional): Starting index for pagination (default: 0)
• rows (optional): Number of results to return (default: 10)

Example queries:

"Find all structures released in October 2025 grouped by experimental method"
"Search for all X-ray crystal structures with resolution better than 2.0 Å"
"Show me the latest 20 cryo-EM structures sorted by release date"
"Find structures containing ligand 'ATP' with specific binding sites"

Search Field Examples

Common searchable fields include:

• 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

Use get_search_schema to discover all available fields and their descriptions.

Development and Advanced Usage

Development Installation

For contributing or development work, first clone the repository and then install in editable mode:

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

Using PyPI installation:

uvx pdbe-mcp-server --server-type pdbe_api_server --transport sse

Using local development:

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

PDBe Graph Database Server

Enables complex relationship queries and network analysis:

Using PyPI installation:

uvx pdbe-mcp-server --server-type pdbe_graph_server --transport sse

Using local development:

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

Neo4j Cypher Query Support

This server supports executing custom Cypher queries against a Neo4j graph database. The pdbe_run_cypher_query tool is only available when the following environment variables are set:

• NEO4J_URL: The Neo4j database URL (e.g., bolt://localhost:7687)
• NEO4J_USERNAME: The Neo4j username
• NEO4J_PASSWORD: The Neo4j password
• NEO4J_DATABASE (optional): The database name. When set, this is passed to the Neo4j driver for Neo4j 4+. For Neo4j 3.5 compatibility, omit this variable to use the default database.

To use this feature, install the neo4j driver:

pip install neo4j

Security: Only read-only queries are allowed (MATCH, OPTIONAL MATCH). Write operations (MERGE, CREATE, DELETE, REMOVE, SET, LOAD CSV, FOREACH) are blocked to prevent accidental data modification.

Example usage:

Execute query: MATCH (s:Structure) WHERE s.PDB_ID = '1abc' RETURN s.PDB_ID as id, s.TITLE as title

The tool response is formatted as JSON by default, but can be converted to TOON format by setting TOON_ENABLED=true.

PDBe Search Server

Provides advanced Solr-based search and analytics capabilities:

Using PyPI installation:

uvx pdbe-mcp-server --server-type pdbe_search_server --transport sse

Using local development:

uv run pdbe-mcp-server --server-type pdbe_search_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

Experimental TOON Output

You can enable experimental TOON-formatted output for PDBe API tool responses by setting the environment variable TOON_ENABLED=true. See the TOON format specification at https://toonformat.dev/.

• If TOON encoding fails for any reason, the server falls back to JSON output.
• This feature is experimental and intended for opt-in usage only.

Troubleshooting

Common Issues

"Command not found" errors:

• Ensure uv is installed and in your PATH
• Verify the full path to uv in your Claude Desktop configuration

Missing tools in Claude:

• Restart Claude Desktop after configuration changes
• Check the Claude Desktop logs for MCP server errors
• Verify JSON syntax in your configuration file

Resources

• Model Context Protocol - Official MCP documentation and specifications
• PDBe API Documentation - Complete API reference and examples
• PDBe Graph Database - Advanced querying and relationship mapping
• Claude Desktop - Download and setup instructions

License

This project is licensed under the Apache License, Version 2.0 - see the LICENSE file for details.

Support

For questions, bug reports, or feature requests:

• Issues: Use the GitHub Issues tracker
• PDBe Helpdesk: Visit the PDBe Help & Support pages