> ## Documentation Index
> Fetch the complete documentation index at: https://bagel.softnanolab.com/llms.txt
> Use this file to discover all available pages before exploring further.

# Simple Peptide Binder

> Stub: BAGEL peptide binder workflow mapped to source scripts

## 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.

## 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`

## Current status

* Status: `Stub`
* Expansion state: planned

## Known dependencies

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

## 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