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Hi,
I am processing lots of sequences in a fasta file but esm3-small model failed on the sequence "EHVAATHKTGLDALAELTGAALNSVEKLSELQFQTVRASLEDSTEQGKRVFDARSLHELTALQSEVSQPTEKLVAYGRHLYQIAAGTHAEWRKVAQTRA"…
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Good morning,
I would like to propose you to share another extremely useful example of AF2 usage. Many scientists are using protein embeddings for downstream tasks (i.e. function prediction). [AF2 …
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感谢您在 GitHub 上提供代码。 我很抱歉用英语写，但我更喜欢这种语言，因为我不确定谷歌翻译是否能正确表达文本。
I have succeed to execute part of your code. Unfortunately, in line 300 of "**Protein_embedding_process**" method in the script "protein_p…
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Hello author,
It is impossible to create the protein embedding files because of an error while saving the file.
It seems the embeddings have different shapes and can not be saved together in a s…
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Hi, I'm trying to run UCE on Marmoset dataset, but the species is not included in the UCE data. I have obtained the protein embedding using ESM2 (36 layers) and the chromosome location of genes in mar…
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Hi~thanks for your nice model. I am trying to get the embedding of a whole protein from the pretrained model, but i'm little confused about which part i should take, do you have any suggestions? Thank…
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from the paper I see that you first embed text with text-embedding-3-large, then you use your trained projection network from the contrastive learning.
Can you also release the pretrained text proj…
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I am currently trying to obtain residue embeddings for protein sequences. The typical workflow involves the following steps:
```
protein = ESMProtein(sequence=sequence)
protein_tensor = self.mode…
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Hello, you have done a great job and thank you for your contribution to the field of protein-based genome representation.
When I was embedding the genome, I used the sample you provided (test.f…
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Hi,
I was checking ESM-3 structure embedding, and ESM-3 sequence embedding, and found that the distance between embeddings is very less ( 0.0001) . I am curious how ESM-3 model is pre-trained with …