Unofficial UniProt MCP Server

What is Unofficial UniProt MCP Server?

An MCP server that provides 26 specialized bioinformatics tools for accessing the UniProt protein database via its REST API, enabling AI assistants and MCP clients to perform protein research, comparative genomics, structural biology, and systems biology analyses.

How to use Unofficial UniProt MCP Server?

Install Node.js v16+, clone the repository, run npm install and npm build, then start with npm start or add the server to an MCP client (e.g., Claude Desktop) using the JSON configuration provided. Docker deployment is also supported: build the image with docker build -t uniprot-mcp-server and run with docker run -i uniprot-mcp-server.

Key features of Unofficial UniProt MCP Server

• 26 distinct bioinformatics tools across eight categories
• Core protein search, info, gene-based search, sequence retrieval, and feature analysis
• Comparative and evolutionary analysis (homologs, orthologs, phylogenetic data)
• Structure and function analysis (3D PDB, domains, variants, sequence composition)
• Biological context tools (pathways, interactions, GO terms, subcellular localization)
• Batch processing and advanced search with multiple filters
• Literature and cross-reference retrieval (external DB links, publications)
• Data export in GFF, GenBank, EMBL, XML formats and URI resource templates

Use cases of Unofficial UniProt MCP Server

• Search UniProt for proteins by name, keyword, or organism (e.g., human insulin)
• Retrieve comprehensive information for a specific protein by accession number
• Find proteins associated with a gene name (e.g., BRCA1) filtered by organism
• Obtain amino acid sequences in FASTA or JSON format
• Analyze functional domains, active sites, and other features of a protein

FAQ from Unofficial UniProt MCP Server

What are the prerequisites for installation?

Node.js v16 or higher and npm or yarn are required.

How do I configure the server in an MCP client like Claude Desktop?

Add the following to your MCP client config: {"mcpServers": {"uniprot": {"command": "node", "args": ["/path/to/build/index.js"], "env": {}}}}.

Which API does this server use?

It integrates with the UniProt REST API (https://rest.uniprot.org), setting a User-Agent header (UniProt-MCP-Server/1.0.0) and a 30‑second timeout.

What output formats are supported?

Results can be returned in JSON, TSV, FASTA, or XML format, depending on the tool.

Is Docker deployment available?

Yes. You can build a Docker image and run it with docker run -i uniprot-mcp-server, or use Docker Compose for easier management.