Dear users,
Because GFP chromophore (CRO) comes from cyclization of three amino acids: S, Y, and G, I am not sure how to model it.
(1) In "Using NCAAs in Protein-Peptide Interface Design", Ornithine can be seen as a modified form of Lys: only one amino acid.
However, CRO includes three amino acids, so there are total three R groups. When preparing rotamer library, CHI angles from three R groups seems confusing.
(2) In "Adding Diverse Noncanonical Backbones to Rosetta: Enabling Peptidomimetic Design", all five cases in this paper are non-peptidic oligomer scaffolds (noncanonical backbones): each oligomer has repeated unit (NC backbone unit). But there is only one CRO in GFP, it is not repeated unit.
If it is possible, could you please give me some hints, or any tutorial on modeling CRO using rosetta?
Many thanks!
Lei