AlphaFold Sovereign MCP

A Model Context Protocol server — an AlphaFold MCP 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 and export tools (results can be persisted through its API; automatic per-invocation persistence is not yet wired).

This is an unfunded, independent open-source project. It is not a service, not certified for any regulated use, and its outputs are research aids that should be reviewed by qualified humans before any clinical or regulatory use.

This project is not affiliated with, endorsed by, or sponsored by Google DeepMind or EMBL-EBI. "AlphaFold" is a trademark of its respective owner and is used here only to describe the public data (the AlphaFold DB API) that this software consumes.

Status: v1.2.0 (Beta). Engineering-validated (730 tests, 100% line and branch coverage). Not yet scientifically validated by independent domain experts; not yet deployed in production. See STATUS.md and LIMITATIONS.md.

What this is

A Python MCP server that:

• Wraps AlphaFold DB, MONDO, HPO, Open Targets, ClinVar, gnomAD, DisGeNET, ChEMBL, and Ensembl behind MCP tool calls. Each call is a thin orchestration over those upstreams; the server does not add scientific judgement.
• Composes upstreams into multi-source workflows: variant cross-reference reports, disease–target landscape summaries, heuristic target-druggability scoring, drug-repurposing candidate ranking, and cross-species structural-distance computation.
• Ships a local SQLite knowledge graph (storage/knowledge_graph.py) with query and export tools. Tool results can be persisted to it through the knowledge-graph API; automatic per-invocation persistence is not yet wired, so the store is populated only when a caller writes to it explicitly.
• Includes a topological-data-analysis (TDA) module that computes persistent-homology fingerprints (Betti numbers β₀, β₁, β₂) over Vietoris-Rips filtrations of Cα coordinates, and an L2-distance comparator between those fingerprint vectors. The full persistent-homology features require the optional

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