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Currently, after the [biotype cleanup](https://github.com/hammerlab/pyensembl/pull/165), only the biotype "protein_coding" is used in the check in [`Transcript.is_protein_coding()`](https://github.com…
joaoe updated
7 years ago
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Hi,
I am attempting to utilize ColabFold to predict the 3D structure of a protein dimer connected by a disulfide bridge.
I understand that AlphaFold can accomplish this using the following comma…
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# AlphaFold2 - ColabFold - Colab DB
Standard AlphaFold pipeline using MMseqs2
[https://colab-db.github.io/notebooks/colabfold/](https://colab-db.github.io/notebooks/colabfold/)
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I am annotating a paper on UPR in pombe.
However, I can't use the existing term
GO:0030968 endoplasmic reticulum unfolded protein response
because it is defined
The series of molecular s…
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It seems there are various cases where we have a GO synonym derived from PR, but not equivalence axiom in GO. Many of these are candidates for missing logical defs, see attachment.
Columns:
- scope
-…
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I am trying to extract the gold struct from the pdb files.
Where and how to read the protein sequence chain and compare it with the sequence struct predicted by the HMM?
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Hey,
I really want to use your tool, because it looks so convenient (and open source which I love). While installing I was only able to get pycontact to work with mdanalysis 0.20.1, because everytime…
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As you said, you want to find HGTs from "Non Metazoa" species to your species
Your example:
Ingroup:
33208: Metazoa
EGP:
6300: Tylenchida
i check that "Metazoa" ranks "kingdom" with "Tylenchid…
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Hi, after downloading your latest model "uniref_embeddings", I found that the dimensionality of the protein word vector is not 100 dimensions, it is greater than 900 dimensions, so. Has the word vecto…
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The histidine kinases of E. coli two-component systems are inner membrane proteins. They often contain a large periplasmic domain for sensing an external signal and they always contain cytoplasmic dom…