Augmented-Nature-UniProt-MCP-Server

Overview

This is a high-quality MCP server that provides comprehensive access to the UniProt protein database through 26 specialized tools. It covers core protein analysis, comparative and evolutionary analysis, structure-function analysis, biological context analysis, batch processing, literature references, and data export capabilities. The server is well-documented with clear installation instructions, examples, and error handling. It's built with TypeScript, includes Docker support, and has been actively maintained with recent commits.

Try asking AI

After installing, here are 6 things you can ask your AI assistant:

• search_proteins

  Search the UniProt database for proteins by name, keyword, or organism.

  Try:Search for insulin proteins in humansTry:Find proteins related to p53 tumor suppressorTry:Search for kinases in mice
• get_protein_info

  Get detailed information for a specific protein by UniProt accession.

  Try:Get detailed information about human insulinTry:Retrieve information for protein accession P01308Try:Tell me about the BRCA1 protein
• search_by_gene

  Search for proteins by gene name or symbol.

  Try:Find proteins associated with the BRCA1 geneTry:Search for proteins from the TP53 geneTry:Show me proteins from the KRAS gene in humans
• get_protein_sequence

  Get the amino acid sequence for a protein.

  Try:Get the amino acid sequence for human insulinTry:Retrieve the sequence for protein P01308Try:Show me the sequence of BRCA1 protein
• get_protein_features

  Get functional features and domains for a protein.

  Try:Get functional domains and features for human insulinTry:Show me the features of protein P01308Try:Analyze the functional domains of BRCA1
• compare_proteins

  Compare multiple proteins side-by-side with sequence and feature analysis.

  Try:Compare human insulin with mouse insulinTry:Compare sequences of BRCA1 and BRCA2 proteinsTry:Analyze differences between p53 and p63 proteins
• get_protein_homologs

  Find homologous proteins across different species.

  Try:Find homologs of human insulin in other speciesTry:Show me proteins homologous to BRCA1 in miceTry:Identify homologous proteins to TP53 in different organisms
• get_protein_structure

  Access 3D structure information from PDB databases.

  Try:Get 3D structure information for human insulinTry:Find PDB entries for BRCA1 proteinTry:Show structural data for protein P01308
• get_protein_pathways

  Retrieve associated biological pathways from KEGG and Reactome.

  Try:Show biological pathways involving human insulinTry:Find pathways associated with BRCA1Try:What pathways is protein P01308 involved in
• batch_protein_lookup

  Efficiently process multiple protein accessions at once.

  Try:Process accessions P01308, P04637, and P04651Try:Get information for BRCA1, TP53, and KRAS proteinsTry:Retrieve data for insulin-related proteins P01308, P01892, and P01323
• advanced_search

  Perform complex queries with multiple filters like length, mass, organism, and function.

  Try:Search for human proteins with mass between 50-60 kDa and signal peptidesTry:Find proteins from bacteria with kinase activityTry:Show me enzymes from human proteins with more than 500 amino acids
• export_protein_data

  Export protein data in specialized formats like GFF, GenBank, EMBL, and XML.

  Try:Export human insulin data in GenBank formatTry:Save BRCA1 protein data in GFF formatTry:Get protein P01308 in XML format

Comparable tools

Installation

git clone <repository-url>
cd uniprot-server

npm install

npm run build

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

FAQ

What data sources does this MCP server use?

This server integrates directly with the UniProt REST API to access protein data, structures, annotations, and related information from the UniProt database.

Can I use this server with other MCP clients besides Claude Desktop?

Yes, this server implements the standard MCP protocol and can be used with any MCP client that supports stdio communication.

What output formats are available for protein data?

The server supports multiple output formats including JSON, TSV, FASTA, and XML for different tools, with JSON being the default.

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