> ## 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.
# MPNN Perplexity
> Score protein sequences by ProteinMPNN perplexity against a fixed backbone; differentiable.
**License:** ProteinMPNN is open source and free for academic and commercial use under an MIT license. Please refer to [the license](https://github.com/dauparas/ProteinMPNN/blob/main/LICENSE) for full terms.
This constraint 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.
```bibtex theme={null}
@article{dauparas2022proteinmpnn,
title={Robust deep learning--based protein sequence design using ProteinMPNN},
author={Dauparas, Justas and Anishchenko, Ivan and Bennett, Nathaniel and Bai, Hua and Ragotte, Robert J and Milles, Lukas F and Wicky, Basile IM and Courber, Alexis and de Haas, Rob J and Bethel, Neville and others},
journal={Science},
volume={378},
number={6615},
pages={49--56},
year={2022},
publisher={American Association for the Advancement of Science},
doi={10.1126/science.add2187}
}
```
Configuration for ProteinMPNN perplexity scoring.
Backbone structure, optional chains\_to\_redesign, and fixed positions for direct ProteinMPNN scoring.
Weights: proteinmpnn (=v\_48\_020), v\_48\_\{002,010,030} noise variants, abmpnn, soluble.
Options: `proteinmpnn`, `v_48_002`, `v_48_010`, `v_48_030`, `abmpnn`, `soluble`
Softmax temperature for relaxing optimizer logits before ProteinMPNN scoring.
Hard one-hot forward pass with soft-probability gradients.
Device for ProteinMPNN execution, e.g. 'cuda' or 'cuda:0'.
Seed for ProteinMPNN decoding-order sampling. None lets proto-tools choose a fresh seed.
Return ProteinMPNN perplexity by default, or raw mean NLL when set to 'nll'.
Options: `nll`, `ppl`
Pre-scale raw logits before ProteinMPNN; gradients are scaled back by the same factor.
Declarative sequence-symbol bias (canonical 20-AA protein) added before ProteinMPNN.
evo-design/proto-language/proto\_language/constraint/sequence\_scoring/mpnn\_perplexity\_constraint.py
dguo8412