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Hello dear BRAKER developers,
1. I want to annotate a fungal genome for which I do not have RNA-seq evidence, so I intend to use proteins as evidence, however, I have doubts about how to use this o…
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Thank you for developing Chroma. Chroma is such an excellent generative AI tool for de novo protein design.
I would like to inquire about how one can use Chroma to design new functional proteins (no…
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I'm doing gene expression analysis of mussel feet kept under different conditions (ocean acidification, warming, and hypoxia) relative to a control and I'm trying to see if the transcripts that code f…
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## What
Error when writing inter-atomic heat flux in netCDF format. Cause of this error: https://github.com/yamatolab/current-calculations-for-proteins/blob/221028322d184fe67a79bbcd61b1b826f2504093/c…
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使用默认的davis数据,我先运行了main_pretraining,发现缺少.npy文件,在一番寻找之后,我发现可能先要运行scripts.py,但是在艰难地装好库之后,提示缺少proteins.txt,请问这个文件应该是什么格式的?能否提供一个能直接运行的版本?
I ran main_pretraining.py, it says it lacks a ".npy" file. Then…
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Hello,
I'm interested in using MutComputeX to generate scoring matrices for several custom design structures. How can I generate the serialized microenvironments and snapshots needed for model inpu…
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The way I understand this is a query that would just get GO Protein nodes without a specific source node
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Hello! Great tool you have developed.
I was curious as to the specific preprocessing steps for the proteomic data. For instance, CPTAC LUAD seems to contain 11485 proteins, where the original was …
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Running the following command:
```bash
python run.py \
--model_type "ligand_mpnn" \
--seed 111 \
--pdb_path "./inputs/1BC8.pdb" \
--out_folder "./outputs/sc_defau…