UniProt MCP Server

A comprehensive Model Context Protocol (MCP) server providing advanced access to the UniProt protein database. This server offers 26 specialized bioinformatics tools enabling AI assistants and MCP clients to perform sophisticated protein research, comparative genomics, structural biology analysis, and systems biology investigations directly through UniProt's REST API.

Developed by Augmented Nature

Features

Core Protein Analysis (5 tools)

Protein Search: Search the UniProt database by protein name, keywords, or organism
Detailed Protein Info: Retrieve comprehensive protein information including function, structure, and annotations
Gene-based Search: Find proteins by gene name or symbol
Sequence Retrieval: Get amino acid sequences in FASTA or JSON format
Feature Analysis: Access functional domains, active sites, binding sites, and other protein features

Comparative & Evolutionary Analysis (4 tools)

Protein Comparison: Side-by-side comparison of multiple proteins with sequence and feature analysis
Homolog Discovery: Find homologous proteins across different species
Ortholog Identification: Identify orthologous proteins for evolutionary studies
Phylogenetic Analysis: Retrieve evolutionary relationships and phylogenetic data

Structure & Function Analysis (4 tools)

3D Structure Information: Access PDB references and structural data
Advanced Domain Analysis: Enhanced domain analysis with InterPro, Pfam, and SMART annotations
Variant Analysis: Disease-associated variants and mutations
Sequence Composition: Amino acid composition, hydrophobicity, and other sequence properties

Biological Context Analysis (4 tools)

Pathway Integration: Associated biological pathways from KEGG and Reactome
Protein Interactions: Protein-protein interaction networks
Functional Classification: Search by GO terms or functional annotations
Subcellular Localization: Find proteins by subcellular localization

Batch Processing & Advanced Search (3 tools)

Batch Processing: Efficiently process multiple protein accessions
Advanced Search: Complex queries with multiple filters (length, mass, organism, function)
Taxonomic Classification: Search by detailed taxonomic classification

Literature & Cross-References (3 tools)

External Database Links: Links to PDB, EMBL, RefSeq, Ensembl, and other databases
Literature References: Associated publications and citations
Annotation Quality: Quality scores and confidence levels for different annotations

Data Export & Utilities (3 tools)

Specialized Export: Export data in GFF, GenBank, EMBL, and XML formats
Accession Validation: Verify UniProt accession number validity
Taxonomic Information: Detailed taxonomic classification and lineage data

Resource Templates

Direct access to protein data via URI templates for seamless integration

Installation

Prerequisites

Node.js (v16 or higher)
npm or yarn

Setup

Clone the repository:

git clone <repository-url>
cd uniprot-server

Install dependencies:

npm install

Build the project:

npm run build

Docker

Building the Docker Image

Build the Docker image:

docker build -t uniprot-mcp-server .

Running with Docker

Run the container:

docker run -i uniprot-mcp-server

For MCP client integration, you can use the container directly:

{
  "mcpServers": {
    "uniprot": {
      "command": "docker",
      "args": ["run", "-i", "uniprot-mcp-server"],
      "env": {}
    }
  }
}

Docker Compose (Optional)

Create a docker-compose.yml for easier management:

version: "3.8"
services:
  uniprot-mcp:
    build: .
    image: uniprot-mcp-server
    stdin_open: true
    tty: true

Run with:

docker-compose up

Usage

As an MCP Server

The server is designed to run as an MCP server that communicates via stdio:

npm start

Adding to MCP Client Configuration

Add the server to your MCP client configuration (e.g., Claude Desktop):

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

Available Tools

1. search_proteins

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

Parameters:

query (required): Search query (protein name, keyword, or complex search)
organism (optional): Organism name or taxonomy ID to filter results
size (optional): Number of results to return (1-500, default: 25)
format (optional): Output format - json, tsv, fasta, xml (default: json)

Example:

{
  "query": "insulin",
  "organism": "human",
  "size": 5
}

2. get_protein_info

Get detailed information for a specific protein by UniProt accession.

Parameters:

accession (required): UniProt accession number (e.g., P04637)
format (optional): Output format - json, tsv, fasta, xml (default: json)

Example:

{
  "accession": "P01308",
  "format": "json"
}

3. search_by_gene

Search for proteins by gene name or symbol.

Parameters:

gene (required): Gene name or symbol (e.g., BRCA1, INS)
organism (optional): Organism name or taxonomy ID to filter results
size (optional): Number of results to return (1-500, default: 25)

Example:

{
  "gene": "BRCA1",
  "organism": "human"
}

4. get_protein_sequence

Get the amino acid sequence for a protein.

Parameters:

accession (required): UniProt accession number
format (optional): Output format - fasta, json (default: fasta)

Example:

{
  "accession": "P01308",
  "format": "fasta"
}

5. get_protein_features

Get functional features and domains for a protein.

Parameters:

accession (required): UniProt accession number

Example:

{
  "accession": "P01308"
}

Resource Templates

The server provides direct access to UniProt data through URI templates:

1. Protein Information

URI: uniprot://protein/{accession}
Description: Complete protein information for a UniProt accession
Example: uniprot://protein/P01308

2. Protein Sequence

URI: uniprot://sequence/{accession}
Description: FASTA format protein sequence
Example: uniprot://sequence/P01308

3. Search Results

URI: uniprot://search/{query}
Description: Search results for proteins matching the query
Example: uniprot://search/insulin

Examples

Basic Protein Search

Search for insulin proteins in humans:

// Tool call
{
  "tool": "search_proteins",
  "arguments": {
    "query": "insulin",
    "organism": "human",
    "size": 10
  }
}

Get Detailed Protein Information

Retrieve comprehensive information about human insulin:

// Tool call
{
  "tool": "get_protein_info",
  "arguments": {
    "accession": "P01308"
  }
}

Gene-based Search

Find proteins associated with the BRCA1 gene:

// Tool call
{
  "tool": "search_by_gene",
  "arguments": {
    "gene": "BRCA1",
    "organism": "human"
  }
}

Retrieve Protein Sequence

Get the amino acid sequence for human insulin:

// Tool call
{
  "tool": "get_protein_sequence",
  "arguments": {
    "accession": "P01308",
    "format": "fasta"
  }
}

Analyze Protein Features

Get functional domains and features for human insulin:

// Tool call
{
  "tool": "get_protein_features",
  "arguments": {
    "accession": "P01308"
  }
}

API Integration

This server integrates with the UniProt REST API for programmatic access to protein data. For more information about UniProt:

UniProt Website: https://www.uniprot.org/
API Documentation: https://www.uniprot.org/help/api
REST API Guide: https://www.uniprot.org/help/api_queries

All API requests include:

User-Agent: UniProt-MCP-Server/1.0.0
Timeout: 30 seconds
Base URL: https://rest.uniprot.org (programmatic access only)

Error Handling

The server includes comprehensive error handling:

Input Validation: All parameters are validated using type guards
API Errors: Network and API errors are caught and returned with descriptive messages
Timeout Handling: Requests timeout after 30 seconds
Graceful Degradation: Partial failures are handled appropriately

Development

Build the Project

npm run build

Development Mode

Run TypeScript compiler in watch mode:

npm run dev

Project Structure

uniprot-server/
├── src/
│   └── index.ts          # Main server implementation
├── build/                # Compiled JavaScript output
├── package.json          # Node.js dependencies and scripts
├── tsconfig.json         # TypeScript configuration
└── README.md            # This file

Dependencies

@modelcontextprotocol/sdk: Core MCP SDK for server implementation
axios: HTTP client for UniProt API requests
typescript: TypeScript compiler for development

License

MIT License

Contributing

Fork the repository
Create a feature branch
Make your changes
Add tests if applicable
Submit a pull request

Support

For issues and questions:

Check the UniProt API documentation
Review the Model Context Protocol specification
Open an issue on the repository

About Augmented Nature

This comprehensive UniProt MCP Server is developed by Augmented Nature, a leading innovator in AI-powered bioinformatics and computational biology solutions. Augmented Nature specializes in creating advanced tools that bridge the gap between artificial intelligence and biological research, enabling researchers to unlock deeper insights from biological data.

Complete Tool Reference

Core Protein Analysis Tools

search_proteins - Search UniProt database by name, keyword, or organism
get_protein_info - Get detailed protein information by accession
search_by_gene - Find proteins by gene name or symbol
get_protein_sequence - Retrieve amino acid sequences
get_protein_features - Access functional features and domains

Comparative & Evolutionary Analysis Tools

compare_proteins - Compare multiple proteins side-by-side
get_protein_homologs - Find homologous proteins across species
get_protein_orthologs - Identify orthologous proteins
get_phylogenetic_info - Retrieve evolutionary relationships

Structure & Function Analysis Tools

get_protein_structure - Access 3D structure information from PDB
get_protein_domains_detailed - Enhanced domain analysis (InterPro, Pfam, SMART)
get_protein_variants - Disease-associated variants and mutations
analyze_sequence_composition - Amino acid composition analysis

Biological Context Tools

get_protein_pathways - Associated biological pathways (KEGG, Reactome)
get_protein_interactions - Protein-protein interaction networks
search_by_function - Search by GO terms or functional annotations
search_by_localization - Find proteins by subcellular localization

Batch Processing & Advanced Search Tools

batch_protein_lookup - Process multiple accessions efficiently
advanced_search - Complex queries with multiple filters
search_by_taxonomy - Search by taxonomic classification

Literature & Cross-Reference Tools

get_external_references - Links to other databases (PDB, EMBL, RefSeq, etc.)
get_literature_references - Associated publications and citations
get_annotation_confidence - Quality scores for annotations

Data Export & Utility Tools

export_protein_data - Export in specialized formats (GFF, GenBank, EMBL, XML)
validate_accession - Check accession number validity
get_taxonomy_info - Detailed taxonomic information

Changelog

v1.0.0 - Comprehensive Bioinformatics Platform

Major expansion: Added 21 new specialized tools (total: 26 tools)
Comparative Analysis: Protein comparison, homolog/ortholog identification, phylogenetic analysis
Structural Biology: 3D structure integration, detailed domain analysis, variant analysis
Systems Biology: Pathway integration, protein interactions, functional classification
Advanced Search: Batch processing, complex filtering, taxonomic search
Literature Integration: External database links, citations, annotation confidence
Data Export: Multiple specialized formats (GFF, GenBank, EMBL, XML)
Enhanced Docker Support: Multi-stage builds with security best practices
Comprehensive Documentation: Complete tool reference and examples
Developed by Augmented Nature: Professional bioinformatics platform

This server cannot be installed

security - not tested

license - permissive license

quality - not tested

UniProt MCP Server

Related MCP Servers

salesforce-mcp
leilaabdel
-
security
F
license
-
quality
Salesforce MCP Server
Last updated -
Python
MISP-MCP-SERVER
bornpresident
-
security
-
license
-
quality
MISP-MCP-SERVER
Last updated -
Python
MarineTraffic MCP Server
Cyreslab-AI
-
security
A
license
-
quality
MarineTraffic MCP Server
Last updated -
1
TypeScript
MIT License
mcp-server-docy
oborchers
-
security
A
license
-
quality
mcp-server-docy
Last updated -
2
Python
MIT License

View all related MCP servers