AlphaFold MCP Server

A comprehensive Model Context Protocol (MCP) server that provides access to the AlphaFold Protein Structure Database through a rich set of tools and resources for protein structure prediction analysis.

Overview

This MCP server enables seamless integration with AlphaFold's vast collection of protein structure predictions, offering tools for structure retrieval, confidence analysis, batch processing, and visualization preparation. Perfect for researchers, bioinformaticians, and structural biologists working with predicted protein structures.

Features

🧬 Core Structure Tools

• Structure Retrieval: Get AlphaFold predictions by UniProt ID
• Multi-format Downloads: Support for PDB, CIF, BCIF, and JSON formats
• Availability Checking: Verify if predictions exist for specific proteins

🔍 Search & Discovery

• Structure Search: Find proteins by name, gene, or organism
• Organism Browsing: List all available structures for specific species
• Coverage Statistics: Get comprehensive organism-level statistics

📊 Confidence & Quality Analysis

• Per-residue Confidence: Detailed confidence scores for each amino acid
• Region Analysis: Identify high/low confidence structural regions
• Quality Validation: Assess overall prediction reliability

⚡ Batch Processing

• Bulk Retrieval: Process multiple proteins simultaneously
• Batch Downloads: Efficient multi-structure downloads
• Parallel Analysis: Confidence analysis for protein sets

🔬 Comparative Analysis

• Structure Comparison: Side-by-side analysis of multiple proteins
• Similarity Search: Find structurally related proteins
• Coverage Comparison: Analyze prediction completeness

🎨 Visualization Integration

• PyMOL Scripts: Ready-to-use visualization scripts
• ChimeraX Integration: Confidence-colored structure viewing
• Custom Export Formats: Flexible data export options

Installation

# Clone or create the server directory
npm install

# Build the server
npm run build

Usage

As MCP Server

Add to your MCP configuration:

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

Direct Usage

# Start the server
npm start

# Or run directly
node build/index.js

Available Tools

Core Structure Tools

get_structure

Retrieve AlphaFold structure prediction for a specific UniProt ID.

Parameters:

• uniprotId (required): UniProt accession (e.g., "P21359", "Q8N726")
• format (optional): Output format - "pdb", "cif", "bcif", or "json" (default: "json")

Example:

{
  "uniprotId": "P04637",
  "format": "json"
}

download_structure

Download AlphaFold structure file in specified format.

Parameters:

• uniprotId (required): UniProt accession
• format (optional): File format - "pdb", "cif", or "bcif" (default: "pdb")

check_availability

Check if AlphaFold structure prediction is available for a UniProt ID.

Parameters:

• uniprotId (required): UniProt accession to check

Search & Discovery Tools

search_structures

Search for available AlphaFold structures by protein name or gene.

Parameters:

• query (required): Search term (protein name, gene name, etc.)
• organism (optional): Filter by organism
• size (optional): Number of results (1-100, default: 25)

list_by_organism

List all available structures for a specific organism.

Parameters:

• organism (required): Organism name (e.g., "Homo sapiens", "Escherichia coli")
• size (optional): Number of results (1-100, default: 50)

get_organism_stats

Get statistics about AlphaFold coverage for an organism.

Parameters:

• organism (required): Organism name

Confidence & Quality Tools

`get_confidence_

... View full README on GitHub