Comments (2)
Hello,
Did you download the Thermostability dataset from here and use the lmdb data from the foldseek
dir? We have provided the datasets for both ESM-2 and SaProt, named normal
and foldseek
respectively.
If you want to fine-tune SaProt you need to load data from the foldseek
dir.
from saprot.
Got it, thank you.
from saprot.
Related Issues (20)
- Why is the length of the SA-token sequence not equal to the length of the model outputs? HOT 1
- EC GO results HOT 3
- pretraining esm2_t33_650M_UR50D HOT 3
- Foldseek can't be used HOT 4
- Finetuning GPU memory cost HOT 2
- Mismatch between ESM2 pretraining dataset and SaProt pretraining dataset HOT 1
- per residue representations HOT 2
- Problem of 'Some weights of EsmForMaskedLM were not initialized from the model checkpoint at ./SaProt_model and are newly initialized' HOT 1
- 'utf-8' codec can't decode byte 0x80 in position 64: invalid start byte HOT 1
- How to use my own dataset HOT 5
- Reproducibility issues - Different scores than the ones from ProteinGym HOT 7
- How to reproduce the SaProt_35M_AF2? HOT 9
- How / where do I tell SaProt to use the fine tuned model? HOT 4
- How can I use Saprot to predict the mutational effects on my own protein? HOT 9
- Inconsistent config in `SaProt_35M_AF2.pt` when loading by the esm implementation HOT 1
- Guideline for fine-tuning a pre-trained model with specific protein thermal stability data HOT 2
- Dataset overlap HOT 2
- How to download cif files? HOT 1
- Output dimension HOT 1
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from saprot.