meok-sequence-lookup-mcp

Protein + structure sequence lookup MCP. Real UniProt REST + RCSB PDB. Ed25519-signed receipts. Hermetic by default (offline tests, live at call time). MIT.

A Model Context Protocol server that wraps two public bioinformatics APIs and returns every result wrapped in an Ed25519-signed envelope so a downstream auditor can verify the response was produced by this build of the server with the public key in meok_sequence_lookup_mcp.server.ISSUER_PUBLIC_KEY_HEX.

It does not interpret, annotate, or recommend — it returns public records verbatim. Downstream tools must not present the outputs as scientific advice.

Honesty register (read first)

This MCP is part of MEOK AI Labs (CSOAI LTD) research tooling. What this MCP does:

• wraps the real, public, free UniProt REST API and RCSB PDB Data API (no mock data);
• signs every result with Ed25519 (so a downstream auditor can verify provenance — this is not a certification, an attestation body, or a scientific-validity claim);
• emits clear rate-limit + attribution notes for the public APIs it wraps.

What this MCP does not claim:

• it is not certified by any scientific-validity, regulatory, or accreditation body;
• it does not provide free compute credits, free-tier access, or partnership terms of any kind (those are commercial questions for the owner of MEOK Labs);
• it is not affiliated with, endorsed by, or sponsored by the UniProt Consortium, the RCSB PDB, the Worldwide Protein Data Bank, or any other public scientific consortium;
• it provides no biological / structural interpretation — results are returned verbatim from the source API.

The 5 tools

Every tool returns a signed envelope:

{
  "status": "ok",
  "tool": "uniprot_search",
  "input": {...},
  "data": {...},
  "issued_at": "2026-07-05T10:00:00Z",
  "kid": "meok-issuer-<hex>",
  "issuer": "meok.ai",
  "signature": "<hex Ed25519>"
}

Verify offline:

from meok_sequence_lookup_mcp.server import verify_envelope, ISSUER_PUBLIC_KEY_HEX
verify_envelope(envelope, envelope["signature"])  # True / False

Install

cd meok-sequence-lookup-mcp
pip install -e ".[dev]"

Run

# As a stdio MCP server (the typical host):
python -m meok_sequence_lookup_mcp.server

Test

cd meok-sequence-lookup-mcp
pytest -q

Tests are hermetic — they do not call the public APIs. To exercise the live APIs, run pytest --live.

Attribution

This MCP wraps:

• UniProt REST API — UniProt Consortium (EBI / SIB / PIR). https://www.uniprot.org/help/programmatic_access
• RCSB PDB Data API — RCSB Protein Data Bank. https://data.rcsb.org/

Per the providers' terms, this MCP identifies itself as meok-sequence-lookup-mcp/0.1.0 in the User-Agent header.

Rate limits (the honest numbers)

• UniProt REST API: no documented hard ceiling, but a polite User-Agent
  • non-parallel batch is recommended. The API returns HTTP 429 when overloaded.
• RCSB PDB Data API: documented at https://www.rcsb.org/docs/programmatic-access; the API returns HTTP 429 when overloaded.

The MCP respects these limits: it sleeps between sequential calls and emits the observed x-ratelimit-* headers (when present) into the envelope metadata.

License

MIT — see LICENSE.