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.

Features

• Search UniProtKB by protein name, gene name or keyword when the accession number is not known yet
• Get protein information by UniProt accession number
• Batch retrieval of multiple proteins
• Get annotated sequence features with their positions: signal peptide, propeptide, mature chain, active and binding sites, disulfide bonds, domains, glycosylation, natural variants and mutagenesis
• Get the available structures: PDB entries with method, resolution and covered residue ranges, plus the AlphaFold DB model
• Caching for improved performance (24-hour TTL), shared across the tools that read the same entry
• Error handling and logging

Requirements

• Python 3.10 or higher
• MCP Python SDK 1.x (mcp>=1.1,<2)

The MCP SDK's 2.0 release removed the @server.list_tools() / @server.call_tool() decorators from the low-level Server class that this project is built on. Installed against mcp 2.x, the server raises AttributeError: 'Server' object has no attribute 'list_tools' at startup, so the dependency is pinned to the 1.x line. Migrating to the 2.x server API is tracked separately.

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

3. Install dependencies:

   # 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?

When you do not have an accession number to hand:

Find the reviewed human phospholipase A2 entries and show me their lengths.

Before designing a construct or a variant panel, to get the boundaries and the residues that have to be respected:

What are the signal peptide, propeptide and mature chain boundaries of P04054,
and where are its active sites and disulfide bonds?

To find a structure to work from:

Which PDB structures cover P04054, and at what resolution?

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
   • A lookup that fails is reported per accession, so one bad entry does not lose the rest of the batch

3. search_proteins

   • Find entries when the accession number is not known yet
   • Required parameter: query (search terms; UniProt query syntax is accepted, e.g. gene:PLA2G1B)
   • Optional: organism_id (NCBI taxonomy ID, e.g. 9606 for human), reviewed_only (default true, Swiss-Prot only), limit (1-50, default 10)
   • Sequences are not included, so a result list stays small
   • Example response:

     {
       "count": 1,
       "results": [
         {
           "accession": "P04054",
           "entry_name": "PA2GA_HUMAN",
           "protein_name": "Phospholipase A2",
           "gene_names": ["PLA2G1B"],
           "organism": "Homo sapiens",
           "taxon_id": 9606,
           "length": 148,
           "reviewed": true
         }
       ]
     }

4. get_protein_features

   • Get the annotated sequence features with 1-based inclusive positions
   • Required parameter: accession
   • Optional: types (keep only these feature types, matched case-insensitively, e.g. ["Active site", "Disulfide bond"]), include_secondary_structure (default false)
   • Secondary structure (Helix, Beta strand, Turn) is reported per element, so an entry carries dozens of them and they say nothing a sequence-design decision needs. They are withheld unless include_secondary_structure is set or they are named in types.
   • Example response:

     {
       "accession": "P04054",
       "length": 148,
       "feature_counts": {"Signal": 1, "Propeptide": 1, "Chain": 1,
                          "Active site": 2, "Disulfide bond": 7},
       "features": [
         {"type": "Signal", "start": 1, "end": 15, "description": ""},
         {"type": "Propeptide", "start": 16, "end": 22,
          "description": "Activation peptide"},
         {"type": "Chain", "start": 23, "end": 148,
          "description": "Phospholipase A2"}
       ]
     }

   • Features are ordered by position. A feature whose position UniProt leaves unset reports null and sorts last.

5. get_protein_structures

   • Get the structures available for a protein
   • Required parameter: accession
   • Example response:

     {
       "accession": "P04054",
       "pdb_entries": [
         {"pdb_id": "3ELO", "method": "X-ray", "resolution": "1.55 A",
          "chains": "A=16-148"},
         {"pdb_id": "6Q42", "method": "X-ray", "resolution": "1.90 A",
          "chains": "A/B=23-148"}
       ],
       "alphafold_id": "P04054"
     }

   • A protein with no solved structure reports an empty list and a null alphafold_id rather than an error

get_protein_info, get_protein_features and get_protein_structures read different parts of the same UniProt entry, so they share one cached request per accession: asking for all three costs a single round trip.

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

3. Install development dependencies:

   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
• pip-audit for dependency vulnerability checks

Run all checks:

black .
isort .
flake8 .
mypy .
bandit -r src/
pip-audit .

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
• Bounds every UniProt request with a timeout (10s connect, 30s total)
• Surfaces UniProt API errors - including 429 rate limiting - as tool errors; there is no automatic retry or backoff
• Provides detailed error messages

Error Handling

The server handles various error scenarios:

• Invalid accession numbers (UniProt answers with 400, not 404)
• API connection issues (network errors)
• Rate limiting (429 responses) - reported to the caller, not retried
• 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