AlphaFold-MCP-Server
Summary
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.
Available Actions(19)
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
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