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Questions tagged [peptide-shaker]

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plot the relation between RMSD and free energy

how can i plot the relation between rmsd and free energy like the image i attached as i need to find the most stable conformation structure for my cycle peptide after finishing REMD simulation
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complete the res type in sdf

I use the diffdock (link to diffdock on github) to dock a peptide with protein and this tool give me a ligand in sdf file format. I traslate this ligand sdf format file to a pdb format file and find ...
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How to do protein quantification with Peptideshaker output (TMT labeled, MS2)?

I have TMT tagged MS2 mass spec run processed with Peptideshaker. I saved the project in a peptideshaker format cpsx. Now, I would like to do the quantification ...
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How to export peptide-shaker data from commandline?

I would like to export the data from Protein-Shaker proteomics analysis software and use it in downstream analysis. For example the overview data, numbers of validated peptides per protein, confidence,...