AlphaFold MCP Server
Server Configuration
Describes the environment variables required to run the server.
| Name | Required | Description | Default |
|---|---|---|---|
No arguments | |||
Instructions
Guidance the server publishes about itself, which clients place ahead of the tool catalog so the model reads it before choosing anything.
This server publishes no instructions, or was last inspected before Glama recorded them.
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 | |
TDQS
Scored across 19 tools
Most tools have distinct purposes, but some overlap exists: 'get_structure' and 'download_structure' could be confused, as both retrieve structure files, though 'download_structure' specifies format. Similarly, 'batch_structure_info' and 'get_prediction_metadata' both provide metadata, but descriptions clarify different focuses. Overall, descriptions help mitigate ambiguity, but a few tools have unclear boundaries.
Tool names follow a highly consistent verb_noun pattern throughout, with clear, descriptive actions (e.g., 'analyze_confidence_regions', 'batch_download', 'check_availability'). All names use snake_case uniformly, and verbs are well-chosen to indicate distinct operations, making the set predictable and readable.
With 19 tools, the count is slightly high but reasonable for the AlphaFold domain, which involves complex workflows like structure retrieval, analysis, visualization, and batch processing. Each tool appears to earn its place by covering specific aspects, though it might feel heavy for simpler use cases.
The tool surface provides comprehensive coverage for AlphaFold structure prediction workflows, including availability checks, retrieval, metadata, confidence analysis, visualization exports, batch operations, and search functions. There are no obvious gaps; agents can perform full CRUD-like operations and advanced analyses without dead ends.