peptide modifications

[buzuddha]

Hiya!

Thanks for such a wonderful package. I'm working with a lot of peptides that I order from GenScript. A lot of these have modifications or are non-natural amino acids (see here).

Is there any possibility to include these in the package? It would help a lot!

Thanks!

[dosorio]

Hi @buzuddha,

Thank you very much for using Peptides. How would you like to include the modifications? Do you know where I can find the physicochemical properties for them?

Please let me know,

Best wishes,

Daniel

[buzuddha]

Hi Daniel,

Ideally there would be a way to include these in the sequence. In GenScript orders they are inside of curly brackets, for instance {CIT} = citruline.

I'll check with the chemists for the physicochemical properties! Are there specific measures in particular you need?

Thanks for getting back to me so quickly!

[dosorio]

Thanks to you! I can allow modifications to pass the QC of the sequences. Depending on the physicochemical properties you can provide, I can modify the functions accordingly. For example, if you can provide us with mass values, I can modify the MW function to return accurate values.

Best wishes,

Daniel

[buzuddha]

To start off, let's work with the non-natural amino acids first. Here is a drop of information about a handful of the common ones used from PubChem and Pepcalc
non-natural AA.txt
.

[buzuddha]

I went through the modifications we have used. This is a non-exhaustive list of modifiers/modified AA's again using PubChem to get properties.
modifications.txt
.

[dosorio]

Thanks! I will work on it.