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Thank you for a very cool model and paper. Reading the code, it's not immediately obvious how to get the embedding for each of the individual models. Also how to get the combined embedding for all thr…
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I followed the install and attempted to run the example to convert a protein sequence to a 3di embedding. I am getting the following issue: 'T5Tokenizer' object has no attribute 'to'. I have tried uni…
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Hi, I tried to run the code, but when running the training command, it outputs the following Error.
`
loading /content/DeepAAI/dataset/corpus/processed_mat/abs_dataset_cls_antibody=344_virus=912_…
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Can you upload the files domain_embedding.gz and protein_domain.gz so i can prepre the fasta file ?
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Hello,
I encountered a ModuleNotFoundError while trying to run the build_dataset_sample.py script in the project.
Here's the error message I received:
python build_dataset_sample.py
Using backen…
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Hello,
Thank you for developing and sharing a unique algorithm for sequence embedding.
I am currently implementing your SGT algorithm for protein embedding.
While reading your paper, I could see …
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Hey,
Where can I find the embeddings produce by AlphaFold as you wrote in your paper?
I want given a protein (amino acid sequence) to be able to get its embedding vector.
Thank you,
Dan
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**when I run this code**
`python datasets/esm_embedding_preparation.py --protein_ligand_csv data/protein_ligand_example_csv.csv --out_file data/prepared_for_esm.fasta `
**I met this notice:**
```
…
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I'm trying to align a custom representation of a protein together with a corresponding substitution matrix.
[aminobert_embedding_no_tokens_mat.txt](https://github.com/soedinglab/MMseqs2/files/9975…
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Thanks for the great paper and model! I see that you have provided the embeddings of CATHe for training, validation and testing sets in Zenodo. I want to ask if a) there is an easy way to get embeddin…