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* phold version: 0.2.0
* Python version: 3.11.9
* Operating System: Ubuntu 22.04.4 LTS (GNU/Linux 5.15.0-101-generic x86_64)
### Description
Hi. I I am trying to annotate viral proteins
I …
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Hi Kaiyi and other authors,
Congratulations on this paper! The results look very promising, and I cannot wait to apply it to my project.
As I just started to run these codes.
In the extract.…
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Hi, I have a PDB file of my protein-ligand complex. I would like to do the following, and I'm wondering if it's easily achievable using OpenMM.
First, I would like to create a script and perform an…
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In the tree, viruses are split into DNA, RNA, and 'other'. I'm not familiar with most of the names under 'other', but wouldn't all viruses fall under DNA or RNA?
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At the top level, 'Archaea' is labeled as 'Archeobacterium':
![image](https://github.com/user-attachments/assets/7b299f3d-7aa6-4830-b860-05bb28f5df69)
NCBI taxonomy lists it as 'Archaea' or 'Arc…
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For a while, we have been avoiding `Protein Group` modelling in the psm and feature in the format. @jpfeuffer triggered this issue a long time ago. Our main tools DIA-NN, OpenMS TMT, and OpenMS LFQ pi…
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After making the protein synthesis function we need to make some sort of heuristic that compares the old genome to the new one. Basically we compare the proteins made by the previous genome and the al…
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Dear author,
Thank you for sharing the code for your wonderful work—it’s really intriguing! I have a question about sampling molecules for my protein. Should I place the PDB file of the pocket in t…
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## Expected Behavior
I am running foldmason with the command below:
easy-msa /workspace/protein/structs /workspace/results_foldmason/protein/result /workspace/results_foldmason/protein/tmpFolder -…
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https://www.pombase.org/data/Protein_data/
Need to decide what is required
PeptideStats.tsv | 2017-11-23 21:10 | 190K |
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Protein_Features.tsv | 2017-10-20 21:35 | 2.8M | …