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Hi Luwei!
I am running the test example, apparently without errors. But this single protein is taking too long (over one hour). Also, while I am using a dedicated GPU (RTX-4090), its utilization is…
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i am using dynamicbind package very frequently it is an excellent package and helped me a lot in my work but suddenly it started giving an error `(dynamicbind) kinshuk@kinshuk-lab:~/Desktop/Anupam/Dyn…
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when I run tokenize_pdb.py, I met this
Traceback (most recent call last):
File "/app/scripts/tokenize_pdb.py", line 108, in
main(
File "/app/scripts/tokenize_pdb.py", line 64, in main
…
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Dear Vadim,
I analysed thermo raw files with DIA-NN 1.8.1 and 1.9. I matched the generated pg_matrix and pr_matrix to find the number of proteotypic peptides for each reported protein in the pg_matri…
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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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Hello,
I have encountered this error while trying the HelixFold3 app.
You can see my JSON file below:
```
{
"entities": [
{
"type": "protein",
"sequence":…
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- The issue is related to the user-provided proteins feature and its associated issues.
- I am trying to use bakta to perform annotation on a phage predicted protein file that used Phanotate. I wa…
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I would like to know how the train.lmdb and valid.lmdb files in the docking_v2/protein_ligand_binding_pose_prediction_v2 directory were processed from the MOAD dataset. I have checked the code and fou…
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Dear Vadim,
I would like to ask a very basic question about Protein.Group in dia-NN. Below is an example of the protein groups extracted from the pg_matrix.
Protein.Group …
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Hello, I encountered an issue as described in the title.
Building Spectral Library using DIA-NN v1.9.1
I created a spectral library using DIA-NN 1.9.1 with the following parameters. The output f…
Mnago updated
1 month ago