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AlphaFold Sovereign MCP

CI License: Apache 2.0 Python 3.10+ MCP Spec 2025-06-18 Tests Coverage

Beta. Engineering-validated (100% line and branch coverage). Scientifically unvalidated by independent domain experts; not yet deployed in production. See Status and Limitations.

A Model Context Protocol server that wraps AlphaFold DB and 8 other public biomedical data sources behind a set of MCP tool calls, backed by a local SQLite knowledge graph with query, export, and traversal tools. The graph loads a curated boot seed automatically when empty and can be extended through its API; there is no automatic per-invocation persistence.

What it does

  • Wraps AlphaFold DB, MONDO, HPO, Open Targets, ClinVar, gnomAD, DisGeNET, ChEMBL, and Ensembl behind MCP tool calls.
  • Composes upstreams into multi-source workflows — variant triage reports, disease–target landscape summaries, drug-repurposing candidates, cross-species structural divergence.
  • Ships a local SQLite knowledge graph with query, export, and traversal tools. It loads a curated boot seed automatically when empty (16 entities and 15 relationships; disable with AFSMCP_DISABLE_KG_SEED=1) and can be extended through its storage API. There is no automatic per-invocation persistence: the analysis tools do not write to the store on their own.

See Tool reference for the full inventory.

What it is not

  • It is not a hosted service.
  • It is not certified for any regulated use.
  • The ACMG/AMP criteria emitted by the variant tools are a draft surface of upstream evidence — not a clinical interpretation.
  • The druggability tier returned by the target-assessment tool is a heuristic — not a validated prediction.

See Limitations for the itemised gap list.

Quick start

git clone https://github.com/smaniches/alphafold-sovereign-mcp
cd alphafold-sovereign-mcp
uv pip install -e .
alphafold-sovereign --self-test      # PASS on the offline BRCA1 fixture

Configure Claude Desktop and the tools become available in conversations. Full instructions: Installation.

Examples

Cite

Machine-readable metadata in CITATION.cff. GitHub renders a "Cite this repository" button in the sidebar of the repo that consumes this file.