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The basic version would basically just be a matrix visualizer, but there are lots of nice visualization extensions possible like interactive highlighting, comparing two maps across the diagonal of the…
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### Setup
I am reporting a problem with Biopython version 1.79, Python version 3.10.6, and operating
system as follows:
3.10.6 (main, Aug 10 2022, 11:40:04) [GCC 11.3.0]
CPython
Linux-5.15.0-…
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Hi,
Let's have a vote here to decide on a project name. You can use the social "+1" feature to add your votes for the various names (see smiley icon).
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Hello there, amazing work! I was reading through the ESM3 preprint and saw that there was some work done to measure the ESM3-open function prediction performance, so I wanted to test the function pred…
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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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Hi,
I used this tool for protein analysis.
I successfully extracted single and pair representations of my target protein using the local version of AlphaFold.
and performed structural distrib…
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I have searched and download 38 proteomes from unipro database, which can't be used directly for this tool. And I found the error occurred after I edit the command_sequence.sh and add the species inf…
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**Is your feature request related to an existing issue or bug?**
no
**Is your new feature related to a general problem?**
Typically annotation of large secretion systems (T3SS, T4SS, T6SS, etc) c…
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Hi there,
I've a simple case where I've loaded a PDB and a ligand, both separately, meaning they have their own components. Now want to be able to select atoms from the ligand, and get the atoms of…
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I would like to know what is the exact dataset used to generate the toy_ppi dataset in example_data folder (input files used to generate the pre-processed dataset). What are the node features availabl…