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I annotated the [S. pyogenes reference](https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_900475035.1/) with bakta, and noticed some oddly named CDS. When I compare bakta's results to the RefSeq annota…
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# Protein Inception | Liam's Blog
Protein design by hallucination. DeepDream, Markov Chain Monte Carlo (MCMC), KL divergence, gradient optimization, scaffolding functional sites, SARS-CoV-2 receptor …
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Hello! I would like to simulate just a membrane using addMembrane(), but I understand you need to supply Modeller with a molecule/object to which it adds the membrane to. Is there a way to not supply …
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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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Hello, I encounter this error when trying to generate the topology:
```
OpenMMException Traceback (most recent call last)
in ()
67
68 # solvate it in 0.15 …
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Hi,
This is regarding protein generation in DiG.
I wanted to know how you obtained the features present in the protein pickle files. As per Appendix B.1 of the paper, the single and pair represe…
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Hi PepQuery users,
I encountered the following error while running the PepQuery in command line with following command -
`java -jar pepquery-2.0.2/pepquery-2.0.2.jar -b Academia_Sinica_LUAD100_…
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A significant number of citations were lost from UniProt and RefSeq protein files. Do Medline files need to be downloaded, or is this a processing error?
```
"id_count_diff","id_count_new","id_co…
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Hello, I am using your pipeline to design hemoglobin binding protein. When I run the code segment "Analyzing diffusion outputs," I encounter the following error. Thank you very much for your help.
…
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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…