Dear Rosetta users,
Is it possible that we could use Rosetta flexpepdock to dock a cyclic peptide (backbone cycle, disulfide cycle, or chemical linker cycle) with non-canonical amino acids to protein target?
It seems we could model the structures for such cyclic peptide with non-canonical amino acids using Rosetta, but I am not sure their docking methods.
If not, could you please recommend a docking program in Rosetta or other software for this application?
Thanks!
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Post Situation:
Hallo Lei,
I had a similar problem and in my experience, FlexPepDock cannot handle peptidic macrocycles with NCAA. Instead, I used the anchor extension approach like in https://www.nature.com/articles/s41467-021-23609-8 and https://www.pnas.org/doi/full/10.1073/pnas.2012800118.
Best,
Yasser
Hallo Yasser,
Thank you very much for your kind reply, I really appreciate it.
I will read them and dock as you suggest.
Best,
Lei