AlphaFold Sovereign MCP server

AlphaFold Sovereign MCP

<!-- mcp-name: io.github.smaniches/alphafold-sovereign-mcp -->

Answering a structural-biology or variant question usually means querying many public databases by hand — AlphaFold DB, Open Targets, ClinVar, gnomAD, and more — and reconciling their formats. This server wraps those sources behind one set of MCP tool calls that run as a local process on your own machine, with no hosted service of ours in the path, no telemetry, and a local SQLite knowledge graph that never leaves your disk. In the default online mode the tools query those public upstreams directly, so the identifiers you look up are sent to them (and one, DisGeNET, needs its own free API key); set ALPHAFOLD_OFFLINE=1 to refuse outbound requests before any socket opens, so no identifier leaves the machine (the knowledge-graph tools still answer from local data; the upstream tools report their source as unavailable). "Sovereign" here means local-first — your compute and stored results stay on your machine — not that the server runs without a network.

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.

Shortened. The full README is on GitHub.