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57 lines
2.9 KiB
Markdown
57 lines
2.9 KiB
Markdown
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_Figure: Comparison of OpenFold and AlphaFold2 predictions to the experimental structure of PDB 7KDX, chain B._
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# OpenFold
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A faithful but trainable PyTorch reproduction of DeepMind's
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[AlphaFold 2](https://github.com/deepmind/alphafold).
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# Documentation
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See our new home for docs at [openfold.readthedocs.io](https://openfold.readthedocs.io/en/latest/), with instructions for installation and model inference/training.
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Much of the content from this page may be found [here.](https://github.com/aqlaboratory/openfold/blob/main/docs/source/original_readme.md)
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## Copyright Notice
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While AlphaFold's and, by extension, OpenFold's source code is licensed under
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the permissive Apache Licence, Version 2.0, DeepMind's pretrained parameters
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fall under the CC BY 4.0 license, a copy of which is downloaded to
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`openfold/resources/params` by the installation script. Note that the latter
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replaces the original, more restrictive CC BY-NC 4.0 license as of January 2022.
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## Contributing
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If you encounter problems using OpenFold, feel free to create an issue! We also
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welcome pull requests from the community.
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## Citing this Work
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Please cite our paper:
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```bibtex
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@article {Ahdritz2022.11.20.517210,
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author = {Ahdritz, Gustaf and Bouatta, Nazim and Floristean, Christina and Kadyan, Sachin and Xia, Qinghui and Gerecke, William and O{\textquoteright}Donnell, Timothy J and Berenberg, Daniel and Fisk, Ian and Zanichelli, Niccolò and Zhang, Bo and Nowaczynski, Arkadiusz and Wang, Bei and Stepniewska-Dziubinska, Marta M and Zhang, Shang and Ojewole, Adegoke and Guney, Murat Efe and Biderman, Stella and Watkins, Andrew M and Ra, Stephen and Lorenzo, Pablo Ribalta and Nivon, Lucas and Weitzner, Brian and Ban, Yih-En Andrew and Sorger, Peter K and Mostaque, Emad and Zhang, Zhao and Bonneau, Richard and AlQuraishi, Mohammed},
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title = {{O}pen{F}old: {R}etraining {A}lpha{F}old2 yields new insights into its learning mechanisms and capacity for generalization},
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elocation-id = {2022.11.20.517210},
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year = {2022},
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doi = {10.1101/2022.11.20.517210},
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publisher = {Cold Spring Harbor Laboratory},
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URL = {https://www.biorxiv.org/content/10.1101/2022.11.20.517210},
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eprint = {https://www.biorxiv.org/content/early/2022/11/22/2022.11.20.517210.full.pdf},
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journal = {bioRxiv}
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}
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```
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If you use OpenProteinSet, please also cite:
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```bibtex
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@misc{ahdritz2023openproteinset,
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title={{O}pen{P}rotein{S}et: {T}raining data for structural biology at scale},
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author={Gustaf Ahdritz and Nazim Bouatta and Sachin Kadyan and Lukas Jarosch and Daniel Berenberg and Ian Fisk and Andrew M. Watkins and Stephen Ra and Richard Bonneau and Mohammed AlQuraishi},
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year={2023},
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eprint={2308.05326},
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archivePrefix={arXiv},
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primaryClass={q-bio.BM}
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}
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```
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Any work that cites OpenFold should also cite [AlphaFold](https://www.nature.com/articles/s41586-021-03819-2) and [AlphaFold-Multimer](https://www.biorxiv.org/content/10.1101/2021.10.04.463034v1) if applicable.
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