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AlphaFold Sovereign MCP

Official

by smaniches Β· Python

MCP server for AlphaFold and 8 other biomedical data sources with a local SQLite knowledge graph

AlphaFold Sovereign MCP (io.github.smaniches/alphafold-sovereign-mcp)

This MCP server provides a unified set of Model Context Protocol tool calls for structural-biology and biomedical variant questions. It wraps AlphaFold DB, Open Targets, ClinVar, gnomAD, and additional sources behind local tooling, using a local process and a SQLite knowledge graph on your machine.

πŸ› οΈ Key Features

  • MCP server for AlphaFold and 8 other biomedical data sources
  • Local process execution on the user’s machine
  • Local SQLite knowledge graph that stays on disk
  • Default β€œonline mode” queries public upstreams directly

πŸš€ Use Cases

  • Querying protein-structure information from AlphaFold-related sources
  • Variant questions requiring consolidation across public biomedical databases
  • Working with knowledge-graph–based provenance

⚑ Developer Benefits

  • Single interface via MCP tool calls for multiple upstream formats
  • Supports workflows involving provenance and variant-analysis
  • Python-tagged integration (per provided topics)

⚠️ Limitations

  • In default online mode, upstream queries rely on direct access to public sources

Topics

alphafoldbioinformaticsclaudeclinvardrug-discoveryknowledge-graphmcpmcp-servermodel-context-protocolprotein-structurevariant-classificationprovenancepythonvariant-analysis