AlphaFold MCP Server

Unclaimed

by Augmented-Nature

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.

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Tools (27)

analyze_confidence_regions

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

batch_confidence_analysis

Analyze confidence scores for multiple proteins.

batch_download

Download multiple structure files.

batch_structure_info

Get structure information for multiple proteins simultaneously.

check_availability

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

compare_structures

Compare multiple AlphaFold structures for analysis.

download_structure

Download AlphaFold structure file in specified format.

export_for_chimerax

Export structure data formatted for ChimeraX visualization.

export_for_pymol

Export structure data formatted for PyMOL visualization.

find_similar_structures

Find AlphaFold structures similar to a given protein.

format

(optional): Output format - "pdb", "cif", "bcif", or "json" (default: "json")

get_api_status

Check AlphaFold API status and database statistics.

get_confidence_scores

Get per-residue confidence scores for a structure prediction.

get_coverage_info

Get information about sequence coverage in the AlphaFold prediction.

get_organism_stats

Get statistics about AlphaFold coverage for an organism.

get_prediction_metadata

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

get_structure

Retrieve AlphaFold structure prediction for a specific UniProt ID.

includeConfidence

(optional): Include confidence score coloring (default: true)

list_by_organism

List all available structures for a specific organism.

organism

(optional): Filter by organism

query

(required): Search term (protein name, gene name, etc.)

search_structures

Search for available AlphaFold structures by protein name or gene.

size

(optional): Number of results (1-100, default: 25)

threshold

(optional): Confidence threshold (0-100)

uniprotId

(required): UniProt accession (e.g., "P21359", "Q8N726")

uniprotIds

(required): Array of UniProt accessions (max 50)

validate_structure_quality

Validate and assess the overall quality of an AlphaFold prediction.