How to fine-tune a pre-trained protein language model on the protein folding task ？
### Feature request


@Rocketknight1, Thanks for releasing the notebook and example of [How to fine-tune a pre-trained protein model](https://github.com/huggingface/notebooks/blob/main/examples/protein_language_modeling.ipynb) and [How to generate protein folds](https://github.com/huggingface/notebooks/blob/main/examples/protein_folding.ipynb). These codes help me quickly apply the SOTA protein structure prediction model. 

However, I wonder what is the best way to train the ESMFold from the scratch. To be specific, I want to finetune the protein language model ESM-2 on the large-scale protein sequence database (e.g. UniRef 90), And I can get a new model for  the downstream protein folding task. 

But I don't know whether it can use the Transformers [Trainer](https://huggingface.co/docs/transformers/training) to implement this function. Hope for your suggestions. 

Thanks in advance!



### Motivation

[HuggingFace Trainer](https://huggingface.co/docs/transformers/training) has provided very convenient functions (e.g training on many GPUs) to fine-tune a pre-trained model. 

Providing a notebook or example to fine-tune the protein language model ESM-2 for the protein folding task may be very helpful for the engineer that works on protein structure prediction. 



### Your contribution

I can work with you to contribute the notebook or example of fine-tune the protein language model ESM-2 for the protein folding task if necessary.
Hi @pengshuang - right now our port of ESMFold is only really usable for inference, and is lacking some of the training code. This happened because we were rushing to launch simultaneously with the release by FAIR, and so we had to launch with a couple of bits missing!

We're working with the team at FAIR to add this, though, and I'll let you know when we have anything to report.<|||||>@Rocketknight1 Thanks for your quick reply. Looking forward to your future work.<|||||>This issue has been automatically marked as stale because it has not had recent activity. If you think this still needs to be addressed please comment on this thread.

Please note that issues that do not follow the [contributing guidelines](https://github.com/huggingface/transformers/blob/main/CONTRIBUTING.md) are likely to be ignored.<|||||>@Rocketknight1  Following up on @pengshuang request.  Was hoping to finetune ESM 2 for Antibodies. How can we plug in the finetuned ESM-2  into ESMFold structure prediction