A comprehensive Model Context Protocol server for accessing AlphaFold Protein Structure Database with advanced protein structure prediction tools
AlphaFold MCP server is a locally run integration for AI assistants that speak the Model Context Protocol. A comprehensive Model Context Protocol server for accessing AlphaFold Protein Structure Database with advanced protein structure prediction tools.
This MCP server enables seamless integration with AlphaFold's vast collection of protein structure predictions, offering tools for structure retrieval, confidence analysis, batch processing, and visualization preparation. Perfect for researchers, bioinformaticians, and structural biologists working with predicted protein structures.
Once AlphaFold is connected, these are the calls the assistant has available:
Multi — format Downloads**: Support for PDB, CIF, BCIF, and JSON formatsMetadata — Prediction versions, dates, and quality informationCross-references — Links to other databases and resourcesget_structure — Retrieve AlphaFold structure prediction for a specific UniProt IDdownload_structure — The download_structure tool exposed by this servercheck_availability — Check if AlphaFold structure prediction is available for a UniProt IDsearch_structures — Search for available AlphaFold structures by protein name or genelist_by_organism — The list_by_organism tool exposed by this serverget_organism_stats — The get_organism_stats tool exposed by this serverget_confidence_scores — Get per-residue confidence scores for a structure predictionanalyze_confidence_regions — Analyze confidence score distribution and identify high/low confidence regionsget_prediction_metadata — Get metadata about the prediction including version, date, and quality metricsSetup follows the usual MCP pattern — install or clone the server, register it in your client's configuration file, restart the client.
Among the database access options, the useful question is rarely "what can it do" but "what does it cost you to run" — permissions, credentials, and how much of your context its toolset consumes. AlphaFold's toolset — Multi, Metadata, Cross-references and 11 more — is a fair guide to whether it matches your workflow. It is maintained by Augmented-Nature; worth a glance at recent repository activity before you build anything load-bearing on it.
SyncDev reviews every entry in this directory against the project's own documentation before publishing, and revisits them as servers change.
| Tool | What it does |
|---|---|
| Multi | format Downloads**: Support for PDB, CIF, BCIF, and JSON formats |
| Metadata | Prediction versions, dates, and quality information |
| Cross-references | Links to other databases and resources |
| get_structure | Retrieve AlphaFold structure prediction for a specific UniProt ID. |
| download_structure | The download_structure tool exposed by this server. |
| 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 | The list_by_organism tool exposed by this server. |
| get_organism_stats | The get_organism_stats tool exposed by this server. |
| 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 | The batch_download tool exposed by this server. |
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