> ## Documentation Index
> Fetch the complete documentation index at: https://proto.evodesign.org/docs/llms.txt
> Use this file to discover all available pages before exploring further.

# FAMPNN Inverse Folding

> FAMPNN structure-conditioned protein sequence design with full-atom sidechain co-generation.

<div class="page-hero">
  <img class="page-hero-banner" src="https://proto-bio.github.io/proto-assets/images/generator/fampnn/hero.png" alt="FAMPNN Inverse Folding" />
</div>

<Note>
  **License:** FAMPNN is open source and free for academic and commercial use under an MIT license. Please refer to [the license](https://github.com/richardshuai/fampnn/blob/main/LICENSE) for full terms.
</Note>

<p class="entity-disclaimer">This generator is open source. Any third-party models, product names, or trademarks referenced are the property of their respective owners, and Proto is not affiliated with them.</p>

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    ```bibtex theme={null}
    @inproceedings{widatalla2025fampnn,
      title={Sidechain conditioning and modeling for full-atom protein sequence design with {FAMPNN}},
      author={Widatalla, Talal and Shuai, Richard W. and Hie, Brian L. and Huang, Po-Ssu},
      booktitle={Proceedings of the 42nd International Conference on Machine Learning},
      year={2025},
      series={PMLR},
      volume={267},
      address={Vancouver, Canada}
    }
    ```
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Protein sequence generator using FAMPNN.

## API Reference

<div class="api-model-section api-model-static api-config-section">
  <div class="api-model-header"><span class="api-model-badge api-config-badge">Config</span><span class="api-model-name">FAMPNNGeneratorConfig</span><a href="https://github.com/evo-design/proto-language/blob/d3b7822f74ea64747cc751a3b2ab1aa6b799ac47/proto_language/generator/fampnn_generator.py#L22" target="_blank" class="func-table-btn func-source-btn api-model-source"><svg width="12" height="12" viewBox="0 0 24 24" fill="none" stroke="currentColor" stroke-width="2" stroke-linecap="round" stroke-linejoin="round"><polyline points="16 18 22 12 16 6" /><polyline points="8 6 2 12 8 18" /></svg> Source</a></div>

  Configuration for FAMPNN inverse-folding generation.

  FAMPNN jointly designs amino-acid identities and sidechain conformations
  conditioned on an input backbone. The generator writes the designed protein
  sequence to the assigned segment and attaches FAMPNN's full-atom output
  structure to `proposal.structure`.

  <ParamField path="structure_inputs" type="array">
    Structure(s) with optional chain, fixed-position, and fixed-sidechain selections.
  </ParamField>

  <ParamField path="output_chain_id" type="string">
    When sampling a multi-chain structure, write only this chain's sequence to the target segment.
  </ParamField>

  <ParamField path="model_variant" type="string" default="0.3">
    FAMPNN checkpoint variant for sequence design.
  </ParamField>

  <ParamField path="temperature" type="number" default="0.1">
    Sampling temperature; lower is greedier and higher is more diverse.
  </ParamField>

  <ParamField path="batch_size" type="integer" default="1">
    Number of sequences to process simultaneously on GPU.
  </ParamField>

  <ParamField path="num_steps" type="integer" default="100">
    Number of iterative unmasking steps for sequence design.
  </ParamField>

  <ParamField path="seq_only" type="boolean" default="False">
    If true, skip sidechain generation during sampling.
  </ParamField>

  <ParamField path="repack_last" type="boolean" default="True">
    Repack sidechains after the final sequence is determined.
  </ParamField>

  <ParamField path="psce_threshold" type="number" default="0.3">
    Only condition on sidechains below this predicted-error threshold during design.
  </ParamField>

  <ParamField path="scn_diffusion_steps" type="integer" default="50">
    Number of sidechain diffusion denoising steps.
  </ParamField>

  <ParamField path="scn_step_scale" type="number" default="1.5">
    Step scale for sidechain diffusion.
  </ParamField>

  <ParamField path="device" type="string" default="cuda">
    Device for model inference.
  </ParamField>

  <ParamField path="verbose" type="boolean" default="False">
    Whether to print FAMPNN progress logs.
  </ParamField>
</div>

## Usage

```python python icon="python" theme={null}
from proto_language.generator import FAMPNNGenerator, FAMPNNGeneratorConfig
from proto_language.core import Segment

config = FAMPNNGeneratorConfig(
    # Configure parameters here
)

generator = FAMPNNGenerator(config)

segment = Segment(length=100, sequence_type="protein")
generator.assign(segment)
generator.sample()
```

## Metadata

| Property                 | Value             |
| ------------------------ | ----------------- |
| Key                      | `fampnn`          |
| Class                    | `FAMPNNGenerator` |
| Category                 | `inverse_folding` |
| Input Type               | `structure`       |
| Uses GPU                 | `True`            |
| Supported Sequence Types | `protein`         |
| Allows Empty Start       | `False`           |
