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 / OSS (MIT)
Capabilities	Read-only

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

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

Sources

Augmented-Nature/UniProt-MCP-Server

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