> ## 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.

# Introduction

> BAGEL — Biomolecular Algorithm for Guidance in Energy Landscapes

BAGEL is a modular, open-source Python framework for programmable protein engineering. It formalizes protein design as optimization over an energy landscape, letting you define arbitrary design objectives as energy terms and explore sequence space with gradient-free Monte Carlo methods.

## Getting started

<Card title="Getting Started" icon="rocket" href="/getting-started" horizontal>
  Install BAGEL and run your first protein design.
</Card>

<Card title="Concepts" icon="diagram-project" href="/concepts" horizontal>
  Understand the energy landscape, system hierarchy, oracles, and Monte Carlo optimization.
</Card>

## Customization

<Columns cols={2}>
  <Card title="Custom Energy Terms" icon="bolt" href="/customization/custom-energy-terms">
    Define your own energy terms to encode design constraints.
  </Card>

  <Card title="Custom Mutation Protocols" icon="shuffle" href="/customization/custom-mutation-protocols">
    Control how BAGEL explores sequence space with custom mutation logic.
  </Card>

  <Card title="Custom Minimizers" icon="chart-line-down" href="/customization/custom-minimizers">
    Implement your own optimization or sampling strategy.
  </Card>

  <Card title="Custom Oracles" icon="eye" href="/customization/custom-oracles">
    Plug in new ML models as oracles for structure, embeddings, or properties.
  </Card>

  <Card title="Custom Callbacks" icon="bell" href="/customization/custom-callbacks">
    Add custom logging, checkpointing, and early stopping to optimization runs.
  </Card>
</Columns>

## Case studies

<Columns cols={2}>
  <Card title="Simple Peptide Binder" icon="link" href="/case-studies/simple-peptide-binder">
    Design a peptide binder from scratch.
  </Card>

  <Card title="Targeting IDRs" icon="crosshairs" href="/case-studies/targeting-intrinsically-disordered-regions">
    Design binders for intrinsically disordered regions.
  </Card>

  <Card title="Enzyme Variants" icon="flask-vial" href="/case-studies/enzyme-variants">
    Design functional enzyme variants with conserved active sites.
  </Card>
</Columns>