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Privacy

Proteus does not include telemetry, analytics, background services, accounts, or credential collection.

What Leaves Your Machine

Some helper scripts contact public scientific APIs when you ask them to resolve or fetch data:

  • uniprot_lookup.py sends gene/protein queries and organism filters to UniProt.
  • fetch_pdb.py and validation_report.py send PDB IDs to RCSB PDB.
  • fetch_alphafold.py and resolve_structure.py may send UniProt accessions or protein-name-derived accessions to AlphaFold DB.
  • ChimeraX and PyMOL may access network resources if you run commands such as fetch, open ... from pdb, or open ... from alphafold.

Local coordinate files remain local unless you explicitly upload, commit, share, or pass them to a tool/API that performs network access.

Generated Files

Proteus may write downloaded structures, JSON reports, renders, or temporary handoff files in your working directory or the output directory you choose. Generated AlphaFold files are ignored by default through .gitignore.

No Secrets Required

The default Proteus workflows do not require API keys. Do not put private tokens, clinical data, proprietary coordinates, or unpublished sequences in repository files unless you intentionally want to publish them.