AlphaFold MCP Server
Server Configuration
Describes the environment variables required to run the server.
| Name | Required | Description | Default |
|---|---|---|---|
No arguments | |||
Capabilities
Server capabilities have not been inspected yet.
Tools
Functions exposed to the LLM to take actions
| Name | Description |
|---|---|
| get_structureB | Get AlphaFold structure prediction for a specific UniProt ID |
| download_structureC | Download AlphaFold structure file in specified format |
| check_availabilityC | Check if AlphaFold structure prediction is available for a UniProt ID |
| search_structuresC | Search for available AlphaFold structures by protein name or gene |
| list_by_organismC | List all available structures for a specific organism |
| get_organism_statsC | Get statistics about AlphaFold coverage for an organism |
| get_confidence_scoresC | Get per-residue confidence scores for a structure prediction |
| analyze_confidence_regionsC | Analyze confidence score distribution and identify high/low confidence regions |
| get_prediction_metadataC | Get metadata about the prediction including version, date, and quality metrics |
| batch_structure_infoC | Get structure information for multiple proteins simultaneously |
| batch_downloadC | Download multiple structure files |
| batch_confidence_analysisC | Analyze confidence scores for multiple proteins |
| compare_structuresC | Compare multiple AlphaFold structures for analysis |
| find_similar_structuresC | Find AlphaFold structures similar to a given protein |
| get_coverage_infoC | Get information about sequence coverage in the AlphaFold prediction |
| validate_structure_qualityC | Validate and assess the overall quality of an AlphaFold prediction |
| export_for_pymolC | Export structure data formatted for PyMOL visualization |
| export_for_chimeraxC | Export structure data formatted for ChimeraX visualization |
| get_api_statusB | Check AlphaFold API status and database statistics |
Prompts
Interactive templates invoked by user choice
| Name | Description |
|---|---|
No prompts | |
Resources
Contextual data attached and managed by the client
| Name | Description |
|---|---|
No resources | |
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