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How can we get attention weights from example sequence and structure?
There were no arguments to get attention weights in transformer blocks, unlike esm2.
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Hello author, I have been following your paper "Towards deep learning sequence-structure co-generation for protein design" recently, and it's very well summarized; I found it quite inspiring. I have a…
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First off, thank you for `sv`, is was a nice surprise!
I'm about to start a `community` template, but before starting I would like to know if you have already some "rules" in mind? Or it will come …
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In https://github.com/veraPDF/veraPDF-library/blob/integration/core/src/main/resources/org/verapdf/pdfa/validation/PDFUA-1.xml there is a rule `For documents that are not strongly structured, as descr…
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I encountered an error while using this method: KeyError: 'XcXgXyXtXyXgXd'. So, I checked the result returned by the get_struc_seq method. The seq, which should store the original amino acid sequence,…
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Hi I would love to be able to run this with wgs sequences, and then again separately with amplicon assembles, so that ultimately I can make 2 trees and compare how they cluster depending on input sequ…
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Hi,
Is it possible to fine-tune or re-train the ESM-3 model with the protein sequence and structure or pdb file, and then apply the fine-tuned model to generate sequence or structure embeddings?
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### Checklist
- [X] I am using an up-to-date version.
- [X] I have read the [documentation](https://github.com/TagStudioDev/TagStudio/blob/main/docs/index.md).
- [X] I have searched existing [issues]…
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## Expected Behavior
I try to transform PDB structures into 3Di sequences. For mini3di (https://github.com/althonos/mini3di/), I used
```
pdb_path = "1xso.cif"
# mini3di
from Bio import PDB
if p…
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Hey Patrick,
I have been using Equinox for one of my projects and up until now it has helped immensely in using JAX effectively and seamlessly.
For this project, I was going to use the model of…