Any examples/documentation about peptide mutations?

[aminsagar]

Hello.
Thanks for this awesome work.
This is related to #72 and #98
I am trying to understand if I can use transformato for a protein-peptide system where there are point mutations in the peptide(15-20 residues).
Sometimes these mutations are to modified amino-acids like methylated and halogenated residues which I have parameterized using gaff2. I currently have the solvated systems in amber parm7 and rst format or converted to psf and crd using parmed.
If gaff/amber is not compatible, I can parameterize modified residues using CGenFF as well.
Is there some documentation about how to handle protein-peptide systems or if I can generate the solvated systems, I can just follow the documentation and treat a protein-peptide system as a normal protein-ligand system?
I would be really grateful for any suggestions.
Best,
Amin.

[JohannesKarwou]

Hi Amin,

Sorry for the very late response!

I'm sorry for the bad documentation concerning point mutations. This is currently a work in progress, but in the future it should be possible to mutate peptides with transformato as long as they have the same overall charge!! (Mutating a positive charged amino acid to a negative will not be possible at this stage)
The final idea would be to be able to handle point mutations exactly like relative binding free energies. Currently, there is no support for amber, but I am working on that as well. If there is support, it would be sufficient if you have a parm7 and rst file.

[amin-sagar]

Thanks @JohannesKarwou for your response.
I look forward to these developments.
Most of the mutations I am interested in conserve overall charge.
Many of them include changing just one hydrogen with a methyl or a halogen group.
I have experimental affinity data for these substitutions which I can correlate the theoretical results with.
If you have a pre-release version at some point, I would be more than happy to run tests and report the results.
Best,
Amin.

[JohannesKarwou]

That sounds like a great use case!
I will let you know if we have something more robust so you can test it!