UniProt

How to Set Up and Use UniProt

UniProt MCP Server is a JavaScript-based MCP server that provides AI assistants with seamless access to the UniProtKB protein database through 26 specialized tools, covering protein search, sequence retrieval, structural analysis, pathway mapping, interaction networks, and cross-database ID mapping across over 200 database types. It connects directly to the UniProt public REST API without requiring any API keys, making it immediately usable for bioinformatics research, drug discovery workflows, and proteomics analysis. Researchers and bioinformaticians use it to query protein data, compare homologs, explore disease variants, and export results in standard formats through natural language conversations.

git clone https://github.com/Augmented-Nature/Augmented-Nature-UniProt-MCP-Server
cd Augmented-Nature-UniProt-MCP-Server

npm install

npm run build

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

{
  "mcpServers": {
    "uniprot": {
      "command": "node",
      "args": ["/Users/yourname/Augmented-Nature-UniProt-MCP-Server/build/index.js"],
      "env": {}
    }
  }
}

- "Search for human insulin proteins in UniProt and show me the top 5 results"
- "Get the full amino acid sequence for protein P01308 in FASTA format"
- "Find all proteins associated with the BRCA1 gene in Homo sapiens"
- "What are the known disease-associated variants for the TP53 protein?"
- "Get Gene Ontology annotations for UniProt entry P04637"
- "Map these RefSeq IDs to UniProt accessions: NP_000537, NP_001119584"
- "Compare the human and mouse versions of the insulin receptor protein side by side"