Uniprot MCP Server

🚀 UniProt MCP Server

A Model Context Protocol (MCP) server that enables language models to retrieve protein information from the UniProt database. This server can be integrated with Claude Desktop and other compatible AI applications.

🚀 Quick Start

This UniProt MCP server allows language models to access protein information from the UniProt database. It can be integrated with Claude Desktop and other AI apps.

✨ Features

• Search UniProt: Search for proteins by name, gene, or other criteria.
• Get Protein Details: Retrieve detailed information about proteins.
• Get Protein Sequences: Obtain amino acid sequences.
• Get Protein Functions: Retrieve functional annotations, including GO terms.
• Get Protein Structures: Find relevant PDB structures.

📦 Installation

1. Clone this repository:

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

2. Create a virtual environment (optional but recommended):

   python -m venv venv
   source venv/bin/activate  # On Windows: venv\Scripts\activate
   

3. Install the dependencies:

   pip install -r requirements.txt
   

💻 Usage Examples

Basic Usage

After setting up, you can ask Claude questions like these:

• "Find proteins related to Alzheimer's disease."
• "Get the sequence of protein P05067 (Amyloid precursor protein)."
• "What are the functions of the TP53 protein?"
• "Is there a known 3D structure for the BRCA1 protein?"

📚 Documentation

Local Setup with Claude Desktop

1. Make the server script executable:

   chmod +x server.py
   

2. Configure Claude Desktop to use this MCP server:
   • On macOS/Linux:

     code ~/Library/Application\ Support/Claude/claude_desktop_config.json
     

   • On Windows:

     code $env:AppData\Claude\claude_desktop_config.json
     

3. Add the following configuration (update the path to match the actual file location):

   {
     "mcpServers": {
       "uniprot": {
         "command": "python",
         "args": [
           "/ABSOLUTE/PATH/TO/uniprot-mcp-server/server.py"
         ]
       }
     }
   }
   

4. Restart Claude Desktop.

Development

To run the server directly for testing:

python server.py

Testing Tools

This project includes two testing tools to verify functionality:

• Server Health Check: Verify that the MCP server starts up correctly without errors.

  python server_health_check.py
  

• UniProt API Test: Test the connectivity to the UniProt API and verify that all API calls work as expected.

  python test_server.py
  

Run these tests before using the server to ensure everything is configured correctly.

🔧 Technical Details

The server can be directly run for testing using the command python server.py. There are also two testing tools to ensure the server and API connectivity work properly.

📄 License

This project is licensed under the MIT license.

🤝 Contribution

Contributions are welcome! Please feel free to submit a Pull Request.

1. Fork the repository.
2. Create a 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.