UniProt MCP Server

A Model Context Protocol (MCP) server that provides access to UniProt protein information. This server allows AI assistants to fetch protein function and sequence information directly from UniProt.

<a href="https://glama.ai/mcp/servers/ttjbai3lpx">

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Features

- Get protein information by UniProt accession number
- Batch retrieval of multiple proteins
- Caching for improved performance (24-hour TTL)
- Error handling and logging
- Information includes:
- Protein name
- Function description
- Full sequence
- Sequence length
- Organism

Quick Start

1. Ensure you have Python 3.10 or higher installed
2. Clone this repository:

   git clone https://github.com/TakumiY235/uniprot-mcp-server.git

   cd uniprot-mcp-server

   

   # Using uv (recommended)

   uv pip install -r requirements.txt

   

   # Or using pip

   pip install -r requirements.txt

   

Configuration

Add to your Claude Desktop config file:

- Windows: %APPDATA%\Claude\claude_desktop_config.json
- macOS: ~/Library/Application Support/Claude/claude_desktop_config.json
- Linux: ~/.config/Claude/claude_desktop_config.json

{
  "mcpServers": {
    "uniprot": {
      "command": "uv",
      "args": ["--directory", "path/to/uniprot-mcp-server", "run", "uniprot-mcp-server"]
    }
  }
}

Usage Examples

After configuring the server in Claude Desktop, you can ask questions like:

Can you get the protein information for UniProt accession number P98160?

For batch queries:

Can you get and compare the protein information for both P04637 and P02747?

API Reference

Tools

1. get_protein_info
- Get information for a single protein
- Required parameter: accession (UniProt accession number)
- Example response:

     {

       "accession": "P12345",

       "protein_name": "Example protein",

       "function": ["Description of protein function"],

       "sequence": "MLTVX...",

       "length": 123,

       "organism": "Homo sapiens"

     }

     

2. get_batch_protein_info
- Get information for multiple proteins
- Required parameter: accessions (array of UniProt accession numbers)
- Returns an array of protein information objects

Development

Setting up development environment

1. Clone the repository
2. Create a virtual environment:

   python -m venv .venv

   source .venv/bin/activate  # On Windows: .venv\Scripts\activate

   

   pip install -e ".[dev]"

   

Running tests

pytest

Code style

This project uses:
- Black for code formatting
- isort for import sorting
- flake8 for linting
- mypy for type checking
- bandit for security checks
- safety for dependency vulnerability checks

Run all checks:

black .

isort .

flake8 .

mypy .

bandit -r src/

safety check

Technical Details

- Built using the MCP Python SDK
- Uses httpx for async HTTP requests
- Implements caching with 24-hour TTL using an OrderedDict-based cache
- Handles rate limiting and retries
- Provides detailed error messages

Error Handling

The server handles various error scenarios:
- Invalid accession numbers (404 responses)
- API connection issues (network errors)
- Rate limiting (429 responses)
- Malformed responses (JSON parsing errors)
- Cache management (TTL and size limits)

Contributing

We welcome contributions! Please feel free to submit a Pull Request. Here's how you can contribute:

1. Fork the repository
2. Create your feature branch (git checkout -b feature/amazing-feature)
3. Commit your changes (git commit -m 'Add some amazing feature')
4. Push to the branch (git push origin feature/amazing-feature)
5. Open a Pull Request

Please make sure to update tests as appropriate and adhere to the existing coding style.

License

This project is licensed under the MIT License - see the LICENSE file for details.

Acknowledgments

- UniProt for providing the protein data API
- Anthropic for the Model Context Protocol specification
- Contributors who help improve this project