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AlphaFold MCP Server

Server Configuration

Describes the environment variables required to run the server.

NameRequiredDescriptionDefault

No arguments

Schema

Prompts

Interactive templates invoked by user choice

NameDescription

No prompts

Resources

Contextual data attached and managed by the client

NameDescription

No resources

Tools

Functions exposed to the LLM to take actions

NameDescription
get_structure

Get 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

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