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Alphafold MCP Server

augmented-nature/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.

View on GitHub

Install

Client configuration

{
  "mcpServers": {
    "alphafold-server": {
      "command": "node",
      "args": [
        "/path/to/alphafold-server/build/index.js"
      ]
    }
  }
}
Author
@augmented-nature
Category
Research & Data, Developer Tools
License
MIT
Updated
Oct 6, 2026

About Alphafold MCP Server

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

  • 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

  • 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

  • Per-residue Confidence: Detailed confidence scores for each amino acid

  • Region Analysis: Identify high/low confidence structural regions

  • Quality Validation: Assess overall prediction reliability

Tools (19)

  • get_structure

    Retrieve AlphaFold structure prediction for a specific UniProt ID.

  • download_structure

    Download AlphaFold structure file in specified format.

  • check_availability

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

  • search_structures

    Search for available AlphaFold structures by protein name or gene.

  • list_by_organism

    List all available structures for a specific organism.

  • get_organism_stats

    Get statistics about AlphaFold coverage for an organism.

  • get_confidence_scores

    Get per-residue confidence scores for a structure prediction.

  • analyze_confidence_regions

    Analyze confidence score distribution and identify high/low confidence regions.

  • get_prediction_metadata

    Get metadata about the prediction including version, date, and quality metrics.

  • batch_structure_info

    Get structure information for multiple proteins simultaneously.

  • batch_download

    Download multiple structure files.

  • batch_confidence_analysis

    Analyze confidence scores for multiple proteins.

  • compare_structures

    Compare multiple AlphaFold structures for analysis.

  • find_similar_structures

    Find AlphaFold structures similar to a given protein.

  • get_coverage_info

    Get information about sequence coverage in the AlphaFold prediction.

  • validate_structure_quality

    Validate and assess the overall quality of an AlphaFold prediction.

  • export_for_pymol

    Export structure data formatted for PyMOL visualization.

  • export_for_chimerax

    Export structure data formatted for ChimeraX visualization.

  • get_api_status

    Check AlphaFold API status and database statistics.

Details on this page are taken from the project's README. Open README

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