Update READMEs for ESMFold and add notebooks (huggingface#20067)

* Update READMEs for ESMFold and add notebooks

* Fix PyCharm formatting

* make fix-copies

README.md

@@ -302,7 +302,7 @@ Current number of checkpoints: ![](https://img.shields.io/endpoint?url=https://h
 1. **[ELECTRA](https://huggingface.co/docs/transformers/model_doc/electra)** (from Google Research/Stanford University) released with the paper [ELECTRA: Pre-training text encoders as discriminators rather than generators](https://arxiv.org/abs/2003.10555) by Kevin Clark, Minh-Thang Luong, Quoc V. Le, Christopher D. Manning.
 1. **[EncoderDecoder](https://huggingface.co/docs/transformers/model_doc/encoder-decoder)** (from Google Research) released with the paper [Leveraging Pre-trained Checkpoints for Sequence Generation Tasks](https://arxiv.org/abs/1907.12461) by Sascha Rothe, Shashi Narayan, Aliaksei Severyn.
 1. **[ERNIE](https://huggingface.co/docs/transformers/model_doc/ernie)** (from Baidu) released with the paper [ERNIE: Enhanced Representation through Knowledge Integration](https://arxiv.org/abs/1904.09223) by Yu Sun, Shuohuan Wang, Yukun Li, Shikun Feng, Xuyi Chen, Han Zhang, Xin Tian, Danxiang Zhu, Hao Tian, Hua Wu.
-1. **[ESM](https://huggingface.co/docs/transformers/model_doc/esm)** (from Meta AI) are transformer protein language models.  **ESM-1b** was released with the paper [Biological structure and function emerge from scaling unsupervised learning to 250 million protein sequences](https://www.pnas.org/content/118/15/e2016239118) by Alexander Rives, Joshua Meier, Tom Sercu, Siddharth Goyal, Zeming Lin, Jason Liu, Demi Guo, Myle Ott, C. Lawrence Zitnick, Jerry Ma, and Rob Fergus. **ESM-1v** was released with the paper [Language models enable zero-shot prediction of the effects of mutations on protein function](https://doi.org/10.1101/2021.07.09.450648) by Joshua Meier, Roshan Rao, Robert Verkuil, Jason Liu, Tom Sercu and Alexander Rives. **ESM-2** was released with the paper [Language models of protein sequences at the scale of evolution enable accurate structure prediction](https://doi.org/10.1101/2022.07.20.500902) by Zeming Lin, Halil Akin, Roshan Rao, Brian Hie, Zhongkai Zhu, Wenting Lu, Allan dos Santos Costa, Maryam Fazel-Zarandi, Tom Sercu, Sal Candido, Alexander Rives.
+1. **[ESM](https://huggingface.co/docs/transformers/model_doc/esm)** (from Meta AI) are transformer protein language models.  **ESM-1b** was released with the paper [Biological structure and function emerge from scaling unsupervised learning to 250 million protein sequences](https://www.pnas.org/content/118/15/e2016239118) by Alexander Rives, Joshua Meier, Tom Sercu, Siddharth Goyal, Zeming Lin, Jason Liu, Demi Guo, Myle Ott, C. Lawrence Zitnick, Jerry Ma, and Rob Fergus. **ESM-1v** was released with the paper [Language models enable zero-shot prediction of the effects of mutations on protein function](https://doi.org/10.1101/2021.07.09.450648) by Joshua Meier, Roshan Rao, Robert Verkuil, Jason Liu, Tom Sercu and Alexander Rives. **ESM-2 and ESMFold** were released with the paper [Language models of protein sequences at the scale of evolution enable accurate structure prediction](https://doi.org/10.1101/2022.07.20.500902) by Zeming Lin, Halil Akin, Roshan Rao, Brian Hie, Zhongkai Zhu, Wenting Lu, Allan dos Santos Costa, Maryam Fazel-Zarandi, Tom Sercu, Sal Candido, Alexander Rives. 
 1. **[FLAN-T5](https://huggingface.co/docs/transformers/model_doc/flan-t5)** (from Google AI) released in the repository [google-research/t5x](https://github.com/google-research/t5x/blob/main/docs/models.md#flan-t5-checkpoints) by Hyung Won Chung, Le Hou, Shayne Longpre, Barret Zoph, Yi Tay, William Fedus, Eric Li, Xuezhi Wang, Mostafa Dehghani, Siddhartha Brahma, Albert Webson, Shixiang Shane Gu, Zhuyun Dai, Mirac Suzgun, Xinyun Chen, Aakanksha Chowdhery, Sharan Narang, Gaurav Mishra, Adams Yu, Vincent Zhao, Yanping Huang, Andrew Dai, Hongkun Yu, Slav Petrov, Ed H. Chi, Jeff Dean, Jacob Devlin, Adam Roberts, Denny Zhou, Quoc V. Le, and Jason Wei
 1. **[FlauBERT](https://huggingface.co/docs/transformers/model_doc/flaubert)** (from CNRS) released with the paper [FlauBERT: Unsupervised Language Model Pre-training for French](https://arxiv.org/abs/1912.05372) by Hang Le, Loïc Vial, Jibril Frej, Vincent Segonne, Maximin Coavoux, Benjamin Lecouteux, Alexandre Allauzen, Benoît Crabbé, Laurent Besacier, Didier Schwab.
 1. **[FLAVA](https://huggingface.co/docs/transformers/model_doc/flava)** (from Facebook AI) released with the paper [FLAVA: A Foundational Language And Vision Alignment Model](https://arxiv.org/abs/2112.04482) by Amanpreet Singh, Ronghang Hu, Vedanuj Goswami, Guillaume Couairon, Wojciech Galuba, Marcus Rohrbach, and Douwe Kiela.

docs/source/en/index.mdx

@@ -90,7 +90,7 @@ The documentation is organized into five sections:
 1. **[ELECTRA](model_doc/electra)** (from Google Research/Stanford University) released with the paper [ELECTRA: Pre-training text encoders as discriminators rather than generators](https://arxiv.org/abs/2003.10555) by Kevin Clark, Minh-Thang Luong, Quoc V. Le, Christopher D. Manning.
 1. **[EncoderDecoder](model_doc/encoder-decoder)** (from Google Research) released with the paper [Leveraging Pre-trained Checkpoints for Sequence Generation Tasks](https://arxiv.org/abs/1907.12461) by Sascha Rothe, Shashi Narayan, Aliaksei Severyn.
 1. **[ERNIE](model_doc/ernie)** (from Baidu) released with the paper [ERNIE: Enhanced Representation through Knowledge Integration](https://arxiv.org/abs/1904.09223) by Yu Sun, Shuohuan Wang, Yukun Li, Shikun Feng, Xuyi Chen, Han Zhang, Xin Tian, Danxiang Zhu, Hao Tian, Hua Wu.
-1. **[ESM](model_doc/esm)** (from Meta AI) are transformer protein language models.  **ESM-1b** was released with the paper [Biological structure and function emerge from scaling unsupervised learning to 250 million protein sequences](https://www.pnas.org/content/118/15/e2016239118) by Alexander Rives, Joshua Meier, Tom Sercu, Siddharth Goyal, Zeming Lin, Jason Liu, Demi Guo, Myle Ott, C. Lawrence Zitnick, Jerry Ma, and Rob Fergus. **ESM-1v** was released with the paper [Language models enable zero-shot prediction of the effects of mutations on protein function](https://doi.org/10.1101/2021.07.09.450648) by Joshua Meier, Roshan Rao, Robert Verkuil, Jason Liu, Tom Sercu and Alexander Rives. **ESM-2** was released with the paper [Language models of protein sequences at the scale of evolution enable accurate structure prediction](https://doi.org/10.1101/2022.07.20.500902) by Zeming Lin, Halil Akin, Roshan Rao, Brian Hie, Zhongkai Zhu, Wenting Lu, Allan dos Santos Costa, Maryam Fazel-Zarandi, Tom Sercu, Sal Candido, Alexander Rives.
+1. **[ESM](model_doc/esm)** (from Meta AI) are transformer protein language models.  **ESM-1b** was released with the paper [Biological structure and function emerge from scaling unsupervised learning to 250 million protein sequences](https://www.pnas.org/content/118/15/e2016239118) by Alexander Rives, Joshua Meier, Tom Sercu, Siddharth Goyal, Zeming Lin, Jason Liu, Demi Guo, Myle Ott, C. Lawrence Zitnick, Jerry Ma, and Rob Fergus. **ESM-1v** was released with the paper [Language models enable zero-shot prediction of the effects of mutations on protein function](https://doi.org/10.1101/2021.07.09.450648) by Joshua Meier, Roshan Rao, Robert Verkuil, Jason Liu, Tom Sercu and Alexander Rives. **ESM-2 and ESMFold** were released with the paper [Language models of protein sequences at the scale of evolution enable accurate structure prediction](https://doi.org/10.1101/2022.07.20.500902) by Zeming Lin, Halil Akin, Roshan Rao, Brian Hie, Zhongkai Zhu, Wenting Lu, Allan dos Santos Costa, Maryam Fazel-Zarandi, Tom Sercu, Sal Candido, Alexander Rives. 
 1. **[FLAN-T5](model_doc/flan-t5)** (from Google AI) released in the repository [google-research/t5x](https://github.com/google-research/t5x/blob/main/docs/models.md#flan-t5-checkpoints) by Hyung Won Chung, Le Hou, Shayne Longpre, Barret Zoph, Yi Tay, William Fedus, Eric Li, Xuezhi Wang, Mostafa Dehghani, Siddhartha Brahma, Albert Webson, Shixiang Shane Gu, Zhuyun Dai, Mirac Suzgun, Xinyun Chen, Aakanksha Chowdhery, Sharan Narang, Gaurav Mishra, Adams Yu, Vincent Zhao, Yanping Huang, Andrew Dai, Hongkun Yu, Slav Petrov, Ed H. Chi, Jeff Dean, Jacob Devlin, Adam Roberts, Denny Zhou, Quoc V. Le, and Jason Wei
 1. **[FlauBERT](model_doc/flaubert)** (from CNRS) released with the paper [FlauBERT: Unsupervised Language Model Pre-training for French](https://arxiv.org/abs/1912.05372) by Hang Le, Loïc Vial, Jibril Frej, Vincent Segonne, Maximin Coavoux, Benjamin Lecouteux, Alexandre Allauzen, Benoît Crabbé, Laurent Besacier, Didier Schwab.
 1. **[FLAVA](model_doc/flava)** (from Facebook AI) released with the paper [FLAVA: A Foundational Language And Vision Alignment Model](https://arxiv.org/abs/2112.04482) by Amanpreet Singh, Ronghang Hu, Vedanuj Goswami, Guillaume Couairon, Wojciech Galuba, Marcus Rohrbach, and Douwe Kiela.

notebooks/README.md

@@ -64,6 +64,8 @@ You can open any page of the documentation as a notebook in colab (there is a bu
 | [How to fine-tune a model on image classification (Torchvision)](https://github.com/huggingface/notebooks/blob/main/examples/image_classification.ipynb) | Show how to preprocess the data using Torchvision and fine-tune any pretrained Vision model on Image Classification | [![Open in Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/huggingface/notebooks/blob/main/examples/image_classification.ipynb)| [![Open in AWS Studio](https://studiolab.sagemaker.aws/studiolab.svg)](https://studiolab.sagemaker.aws/import/github/huggingface/notebooks/blob/main/examples/image_classification.ipynb)|
 | [How to fine-tune a model on image classification (Albumentations)](https://github.com/huggingface/notebooks/blob/main/examples/image_classification_albumentations.ipynb) | Show how to preprocess the data using Albumentations and fine-tune any pretrained Vision model on Image Classification | [![Open in Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/huggingface/notebooks/blob/main/examples/image_classification_albumentations.ipynb)| [![Open in AWS Studio](https://studiolab.sagemaker.aws/studiolab.svg)](https://studiolab.sagemaker.aws/import/github/huggingface/notebooks/blob/main/examples/image_classification_albumentations.ipynb)|
 | [How to perform zero-shot object detection with OWL-ViT](https://github.com/huggingface/notebooks/blob/main/examples/zeroshot_object_detection_with_owlvit.ipynb) | Show how to perform zero-shot object detection on images with text queries| [![Open in Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/huggingface/notebooks/blob/main/examples/zeroshot_object_detection_with_owlvit.ipynb)| [![Open in AWS Studio](https://studiolab.sagemaker.aws/studiolab.svg)](https://studiolab.sagemaker.aws/import/github/huggingface/notebooks/blob/main/examples/zeroshot_object_detection_with_owlvit.ipynb)|
+| [How to fine-tune a pre-trained protein model](https://github.com/huggingface/notebooks/blob/main/examples/protein_language_modeling.ipynb) | See how to tokenize proteins and fine-tune a large pre-trained protein "language" model | [![Open in Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/huggingface/notebooks/blob/main/examples/protein_language_modeling.ipynb) | [![Open in AWS Studio](https://studiolab.sagemaker.aws/studiolab.svg)](https://studiolab.sagemaker.aws/import/github/huggingface/notebooks/blob/main/examples/protein_language_modeling.ipynb) |
+| [How to generate protein folds](https://github.com/huggingface/notebooks/blob/main/examples/protein_folding.ipynb) | See how to go from protein sequence to a full protein model and PDB file | [![Open in Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/huggingface/notebooks/blob/main/examples/protein_folding.ipynb) | [![Open in AWS Studio](https://studiolab.sagemaker.aws/studiolab.svg)](https://studiolab.sagemaker.aws/import/github/huggingface/notebooks/blob/main/examples/protein_folding.ipynb) |
 
 ### TensorFlow Examples