Unofficial 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

1. Clone the repository:

git clone <repository-url>
cd uniprot-server

2. Install dependencies:

npm install

3. 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: tru

... [View full README on GitHub](https://github.com/Augmented-Nature/Augmented-Nature-UniProt-MCP-Server#readme)