AlphaFold MCP Server

by Augmented-Nature

Recommended

23 stars

20 downloads

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GitHub

About

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.

Details

Author: Augmented-Nature
Repository: Augmented-Nature/AlphaFold-MCP-Server
GitHub stars: 23
Downloads: 20
License: Other
Categories: Database, Other, Search
Tags: #bioinformatics, #research, #study

Setting up with Highlight

This MCP is not yet compatible with Highlight’s one-click setup. However, you can still use it with Highlight by following these steps:

Download and install Highlight from highlightai.com/download
Navigate to the plugins tab and select "Add Custom Plugin"
Configure the plugin with the settings below
Plugin Name AlphaFold MCP Server

Command (node, npx, python, etc.) node
Arguments
- Argument 1 /path/to/alphafold-server/build/index.js
Please refer to the README for specific instructions on how to obtain API keys or other required environment variables.
Enable "Start Automatically" if you want the plugin to start when Highlight launches

Setting up with Cursor

Open Cursor's settings
Navigate to the MCP section
Click "Add new Global MCP server"
Copy and paste the configuration below based on your operating system

JSON

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

JSON

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

JSON

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

Setting up with Claude Desktop

Open Claude Desktop's settings
Go to the Integrations tab
Click "Add MCP Server"
Use the configuration below based on your operating system

Note: Make sure Claude Desktop is running before attempting to connect.

JSON

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

JSON

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

JSON

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

Setting up with Windsurf

Open Windsurf's preferences
Go to the Integrations section
Click "Add MCP Integration"
Use the configuration below based on your operating system

JSON

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

JSON

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

JSON

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

Setting up with Cline

Open Cline's settings
Navigate to the Integrations section
Click "Add MCP Server"
Copy and paste the configuration below based on your operating system

Note: Make sure to restart Cline after adding the configuration.

JSON

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

JSON

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

JSON

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

Setting up with Goose

Open Goose's preferences
Go to the Integrations tab
Select "MCP Servers"
Click "Add New Server"
Use the configuration below based on your operating system

JSON

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

JSON

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

JSON

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

From the repository

```bash

`get_structure`

Retrieve AlphaFold structure prediction for a specific UniProt ID. Parameters: uniprotId (required), format (optional)

`download_structure`

Download AlphaFold structure file in specified format. Parameters: uniprotId (required), format (optional)

`check_availability`

Check if AlphaFold structure prediction is available for a UniProt ID. Parameters: uniprotId (required)

`search_structures`

Search for available AlphaFold structures by protein name or gene. Parameters: query (required), organism (optional), size (optional)

`list_by_organism`

List all available structures for a specific organism. Parameters: organism (required), size (optional)

`get_organism_stats`

Get statistics about AlphaFold coverage for an organism. Parameters: organism (required)

`get_confidence_scores`

Get per-residue confidence scores for a structure prediction. Parameters: uniprotId (required), threshold (optional)

`analyze_confidence_regions`

Analyze confidence score distribution and identify high/low confidence regions. Parameters: uniprotId (required)

`get_prediction_metadata`

Get metadata about the prediction including version, date, and quality metrics. Parameters: uniprotId (required)

`batch_structure_info`

Get structure information for multiple proteins simultaneously. Parameters: uniprotIds (required), format (optional)

`batch_download`

Download multiple structure files. Parameters: uniprotIds (required), format (optional)

`batch_confidence_analysis`

Analyze confidence scores for multiple proteins. Parameters: uniprotIds (required)

`compare_structures`

Compare multiple AlphaFold structures for analysis. Parameters: uniprotIds (required)

`find_similar_structures`

Find AlphaFold structures similar to a given protein. Parameters: uniprotId (required), organism (optional)

`get_coverage_info`

Get information about sequence coverage in the AlphaFold prediction. Parameters: uniprotId (required)

`validate_structure_quality`

Validate and assess the overall quality of an AlphaFold prediction. Parameters: uniprotId (required)

`export_for_pymol`

Export structure data formatted for PyMOL visualization. Parameters: uniprotId (required), includeConfidence (optional)

`export_for_chimerax`

Export structure data formatted for ChimeraX visualization. Parameters: uniprotId (required), includeConfidence (optional)

`get_api_status`

Check AlphaFold API status and database statistics. Parameters: None

Claude Desktop / Cursor

Paste into your MCP client config file to install this server.

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

Linux

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

Macos

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

Windows

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

AlphaFold MCP Server

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

```bash

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Details

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Setting up with Highlight

From the repository

get_structure

download_structure

check_availability

search_structures

list_by_organism

get_organism_stats

get_confidence_scores

analyze_confidence_regions

get_prediction_metadata

batch_structure_info

batch_download

batch_confidence_analysis

compare_structures

find_similar_structures

get_coverage_info

validate_structure_quality

export_for_pymol

export_for_chimerax

get_api_status

Claude Desktop / Cursor

Linux

Macos

Windows

AlphaFold MCP Server

Overview

Features

🧬 Core Structure Tools

🔍 Search & Discovery

📊 Confidence & Quality Analysis

⚡ Batch Processing

🔬 Comparative Analysis

🎨 Visualization Integration

Installation

Install

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`get_structure`

`download_structure`

`check_availability`

`search_structures`

`list_by_organism`

`get_organism_stats`

`get_confidence_scores`

`analyze_confidence_regions`

`get_prediction_metadata`

`batch_structure_info`

`batch_download`

`batch_confidence_analysis`

`compare_structures`

`find_similar_structures`

`get_coverage_info`

`validate_structure_quality`

`export_for_pymol`

`export_for_chimerax`

`get_api_status`