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Thanks for amazing notebook!
Support for cyclic peptides was recently proposed here:
https://www.biorxiv.org/content/10.1101/2023.02.25.529956v1
It's already supported in ColabDesign but not in…
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Would it make sense to utilise PoET for binding affinity prediction (ic50 score) of short peptide sequences (8-16 amino acids)? If yes, do you have any suggestions/comments on how to do it? Is it poss…
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Dear authors, congratulations on your very nice work!
I have one problem.
Could I use the TULIP model to compare the binding strength of different peptides (such as random peptides) given a fix…
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I encountered an error while using this method: KeyError: 'XcXgXyXtXyXgXd'. So, I checked the result returned by the get_struc_seq method. The seq, which should store the original amino acid sequence,…
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I tested on the test dataset of nextneopi (https://github.com/icbi-lab/nextNEOpi). I has a similar session for using the arriba to get the fusion genes. From those fusion genes, it can get the peptide…
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Currently, pVACseq does not prefilter transcripts on their biotype. We prioritize protein_coding transcripts when picking the best peptide and transcript in the aggregate report creation.
In pVACsp…
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```
In the current specification it's stated (page 26): "The protein's accession
the peptide is associated with. In case no protein section is present in the
file or the peptide was not assigned to …
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Hi, thank you for developing such an excellent software.
### pVACseq: Discrepancy between {sample_id}.all_epitopes.tsv and {sample_id}.fasta ?
#### Description
I have successfully run pVACse…
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We are simulating DIA data (using synthedia https://github.com/mgleeming/synthedia/) and putting it through FragPipe. When we simulate "perfect" fragmentation of spectras, it fail at PeptideProphet an…
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I have the same issue with this #1310 unable to resolve. The error happens when searching specific PTM modifications search, like below. I used TMT11 plex. The monoisotopic mass of 156.1151 on CHK and…