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dosorio / Peptides

An R package to calculate indices and theoretical physicochemical properties of peptides and protein sequences.
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Is the descriptor calculation a simple sum of each amino acid? #48

Open jckkvs opened 2 years ago

jckkvs commented 2 years ago

Is the descriptor calculation a simple sum of each amino acid?

I confirmed that the charge etc. are calculated by simple sum

dosorio commented 2 years ago

Hi @jckkvs, thanks for using Peptides!. Each descriptor is computed as described in the documentation. Some of them are the sum, others the average or a specific formula.

jckkvs commented 2 years ago

Hi @dosorio , thanks for reply and great library.

Is the documentation "https://peptides.readthedocs.io/en/stable/api.html" ? Is my understanding correct?

(sum or average) blosum_indices : The computed average cruciani_properties() : The computed average fasgai_vectors : The computed average

(specific) hydrophobic_moment hydrophobic_moment_profile

The content below is my personal interest and you can ignore it.

If the peptide lengths are the same, I think the average and total have almost the same meaning. We were considering the features when the same amino acids were added to both ends of all peptides in the dataset. (Difference between before and after adding amino acids to both ends)

dosorio commented 2 years ago

Hi @jckkvs, it seems you are using the python version of the package. Please note that project is in no way not affiliated, sponsored, or otherwise endorsed by the original Peptides authors. It was developed by Martin Larralde during his PhD project at the European Molecular Biology Laboratory in the Zeller team.