UniProt MCP Server

MCP wrapper over the UniProt REST API — the standard protein-annotation layer linking sequence, structure, function, and cross-references to other databases.


Type	MCP server
Supplier	Augmented Nature (community OSS)
Availability	GA
Pricing	Free to use — wraps the public UniProt REST API, no auth. Unverified — redistribution terms are contradictory upstream: the committed `LICENSE` file is a restrictive non-commercial grant while `package.json` and the README say MIT.
Capabilities	Read-only
Verified	works · 2026-07-29
Security	caution · 2026-07-29 — committed LICENSE is restrictive non-commercial while page/package.json claim MIT; ~7mo stale

How to install

Also packaged in the SciAgent-Skills collection (jaechang-hits (community OSS, CC BY 4.0)): clone jaechang-hits/SciAgent-Skills and run /plugin install sciagent-skills in Claude Code (or copy skills/proteomics-protein-engineering/uniprot-protein-database into ~/.claude/skills/).
```
git clone https://github.com/Augmented-Nature/UniProt-MCP-Server
cd UniProt-MCP-Server
npm install
npm run build
```

Then add to claude_desktop_config.json (replace /path/to/UniProt-MCP-Server with the absolute path of your clone — e.g., /Users/you/repos/UniProt-MCP-Server):

{
  "mcpServers": {
    "uniprot": { "command": "node", "args": ["/path/to/UniProt-MCP-Server/build/index.js"] }
  }
}

For Claude Code, the equivalent registration is:

claude mcp add --transport stdio uniprot -- node /path/to/UniProt-MCP-Server/build/index.js

Docker alternative: docker build -t uniprot-mcp-server . && docker run -i uniprot-mcp-server.

What it does

26 tools across:

Core protein analysis — search, get by accession, sequence and feature retrieval.
Comparative / evolutionary — orthologs, taxonomy, phylogeny.
Structure / function — domain, PTM, active-site annotation; AlphaFold cross-references.
Biological context — pathways, GO terms, subcellular localization.
Batch search and cross-reference resolution.
Export — FASTA, GFF, GenBank, EMBL, TSV, XML, JSON.

Primary use cases: Resolve gene-to-protein-to-domain context for a hit list; pull orthologs and PTMs; build cross-reference tables for a target panel.

Notes

Claude Science: This resource is offered inside Anthropic’s Claude Science via the Genes & Ontologies featured connector. Its inclusion there is an independent signal of quality and trustworthiness for life-science research.

stdio transport. No auth required — calls the public UniProt REST API. Complements ChEMBL (small molecules) and AlphaFold (3D) by covering the annotation layer.

Upstream licensing is inconsistent (see Pricing above) and the last push was 2025-12-21. Running the server is unproblematic — it is a thin read-only client over a public API — but do not vendor or redistribute the code until the terms are clarified. The SciAgent-Skills packaging above (CC BY 4.0) is a cleanly-licensed alternative route to the same UniProt REST surface.

Sources

Augmented-Nature/UniProt-MCP-Server

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