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Objective

Stub page for the BAGEL peptide-binder design workflow. This page is intentionally source-mapped only and will be expanded into a full tutorial later.

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Source scripts

  • bagel/scripts/binders/simple_binder.py
  • bagel/scripts/technical-report/binders/ca4.py
  • bagel/scripts/technical-report/binders/derf7.py
  • bagel/scripts/technical-report/binders/egfr.py

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Current status

  • Status: Stub
  • Expansion state: planned

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Known dependencies

  • BAGEL (biobagel) installation
  • Oracle backend: Modal (use_modal=True) or local GPU (use_modal=False)
  • ESMFold oracle for structure-driven energy terms

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Expansion checklist

  • Add runnable end-to-end script with explicit parameters
  • Add expected outputs (energies.csv, FASTA, CIF)
  • Add troubleshooting for Modal/local execution
  • Add result-interpretation section for binder quality