Unofficial UniProt MCP Server

@Augmented-Nature

Repository

Basic information

About Unofficial UniProt MCP Server

A comprehensive Model Context Protocol (MCP) server providing advanced access to the UniProt protein database.

#bioinformatics#proteomics#drug-discovery

Unofficial UniProt MCP Server config

Add this server to your MCP-compatible client using the configuration below.

{
  "mcpServers": {
    "augmented-nature-uniprot-mcp-server-augmented-nature": {
      "command": "docker",
      "args": [
        "build",
        "-t",
        "uniprot-mcp-server",
        "."
      ]
    }
  }
}

Unofficial UniProt MCP Server tools

Tool list not available yet

This listing does not currently have a tool list to display. This does not mean the server has no tools; check its documentation for supported capabilities.

We auto-extract tools from the README. The maintainer can list them under a ## Tools heading to populate this section.

Overview

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

Frequently asked questions

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.

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