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![image](https://github.com/user-attachments/assets/6eaebdd2-c690-426c-9a50-3a15919b94ae)
output of Chai-1
![image](https://github.com/user-attachments/assets/a9c10788-ea51-40c7-b011-908c9ad1716b)
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I am seeing an issue with foldseek version "v9.427df8a" when using "--format-mode 3" to generate an html output. In some cases the interactive protein alignment visualization is missing from the outpu…
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These genes have had revised structures which means that they
These genes do not have signal peptides because the sequence does not match the UniProt sequence at the N-term.
https://www.pombas…
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Thanks for your work. However, as I tried to conduct protein structure clustering, the program always returns clusters based on proteins' substructure. I am wondering how can I get the cluster based o…
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Hi,
This is a great work and I would like to have a feature request (or please let me know how to do this if already possible).
Sometimes I do my own alignemnts, and would only like to have the …
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[Class `ProteinEmbedding`](https://github.com/scikit-bio/scikit-bio/blob/545c9859635a5b8514bd9fd599475717c533f108/skbio/embedding/_protein.py#L29-L121) implements a data structure for the storage of p…
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I am only focusing on the standard runs of `-mm 5` and `-mm 6` for two monomeric protein structures. I want to remove all extraneous parameters that are currently implemented in USalign's code base (i…
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## Expected Behavior
database to database "foldseek search" alignment using foldseek-mpi
## Current Behavior
The structure alignment step dies after it sets up the jobs for the structural alignme…
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Hi tfold team,
I applied tFold-ag to the AbDB dataset, and while it performs well on some proteins, I encountered difficulties predicting other proteins. Upon inspecting the predicted structures, …
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https://doi.org/10.1101/137828
> Understanding the relationship between protein structure and function is a fundamental problem in protein science. Given a protein of unknown function, fast identif…