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Hi,
I'm using pyPept to build simple peptide macrocycles. I'm finding the BILN notation extremely useful for this and the pyPept interface is very straightforward to use.
Unfortunately, there se…
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First of all, thank you for your excellent work. I am very interested in your ideas and tools. I have some questions when reading the peptide docking part. I know a tool specifically for peptide docki…
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Dear Vadim,
I searched top-ABPP DIA files with FragPipe to collect a file fold named "diann-output". My question is whether the quantification of assigned modified peptides also is generated from "…
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Carbamidomethyl (C residues) : 57.021464
Of Methionine Oxidation 15.994915
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Hi ! I am pretty interested in the code for cyclic peptide generation and found that the server for CycloPs is down. Is it possible to share the python 3 version of CycloPs you build? Many thanks.
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Per the [deprecation guidelines](https://github.com/microbiomedata/nmdc-schema/blob/a5c3f4e7fe221b01d24151e536bfe00cbeb3ac19/src/docs/schema_element_deprecation_guide.md#L4), we should move the follow…
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Thank you for your work.
When I run vadr 1.6.3 on this virus: https://www.ncbi.nlm.nih.gov/nuccore/KY933089 (fasta file)
I obtain nothing in the 'pass' tsv file.
In the 'fail' tsv file, I get t…
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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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How to predict the structure of cyclic peptides (amide bonds forming a ring)
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Dear @douweschulte,
I have been trying out the version 0.9.0a1 you made previously for the panicked thread error, but I ran into an error when trying to annotate a spectrum with a proforma peptide.…