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Quickstart

Install

# From PyPI (distribution name is uniprot-mcp-server,
# the installed console script is uniprot-mcp):
pip install uniprot-mcp-server
# or in an isolated environment:
uvx --from uniprot-mcp-server uniprot-mcp

# From source:
git clone https://github.com/smaniches/uniprot-mcp.git
cd uniprot-mcp
pip install -e .

Verify it works

uniprot-mcp --self-test

Expected output:

[tools] registered: 41/41
[live] P04637 -> TP53 OK
[PASS]

The self-test makes one live UniProt call (/uniprotkb/P04637) and asserts the gene is TP53. No API key required.

Hook it up to Claude Desktop

Edit claude_desktop_config.json (the location depends on your OS; on Windows it lives under %APPDATA%\Claude\):

{
  "mcpServers": {
    "uniprot": {
      "command": "uniprot-mcp"
    }
  }
}

Restart Claude Desktop. Type /mcp in any conversation; you should see the 41 tools listed.

For strict release pinning (any drift raises an error):

{
  "mcpServers": {
    "uniprot": {
      "command": "uniprot-mcp",
      "args": ["--pin-release=2026_01"]
    }
  }
}

For the local provenance cache (replay any past answer offline):

{
  "mcpServers": {
    "uniprot": {
      "command": "uniprot-mcp",
      "env": {
        "UNIPROT_MCP_CACHE_DIR": "/path/to/your/cache"
      }
    }
  }
}

Hook it up to Claude Code (CLI)

claude mcp add uniprot -- uniprot-mcp

First useful question

Once configured, ask Claude something like:

What does UniProt say about TP53? Resolve any PDB structures.

Claude will call uniprot_get_entry("P04637") followed by uniprot_resolve_pdb("P04637") and present the entry summary plus a structured table of PDB structures (id + method + resolution + chain coverage). Every response carries the provenance footer at the bottom — the line beginning _Source: UniProt release …_ — that you can use later to verify the answer.

A workflow that's hard without uniprot-mcp

For human TP53, give me: (a) the canonical entry summary, (b) a drug-target dossier, (c) a list of every disease association with OMIM IDs, (d) the AlphaFold pLDDT confidence summary, (e) every ClinVar pathogenic variant.

That's five tool calls — uniprot_get_entry, uniprot_target_dossier, uniprot_get_disease_associations, uniprot_get_alphafold_confidence, uniprot_resolve_clinvar — and the agent assembles the answer with provenance footers on every section. See recipes for worked examples.

Where to go next