RosettaCommons
Possible to specify secondary structure for specific part of a diffused protein without using fold conditioning on defined scaffolds
I would like to use RFdiffusion to design an alpha-helical linker between one protein and another protein. Is there a way to specify that a certain part of a design should be alpha-helical without fold conditioning on a specific protein scaffold? My current thought is to use motif scaffolding with the following contig:
'contigmap.contigs=[A1-100/70-150/B1-100/70-150/A101-200]'
Where chain A is the first protein I want to link and chain B is the second. Here, the link to chain B is being inserted in place of a loop in chain A (i.e. primary structure will be ProteinA(first half)-alphaHelicalLinker-ProteinB-alphaHelicalLinker-ProteinA(second half).
I currently cannot see a way to specify that the linker ('contigmap.contigs=[A1-100/70-150/B1-100/70-150/A101-200]') must be alpha helical. Is it possible to do this in an easy way at the command line or do I need to do something janky with a dummy pdb to fold condition on for the linker region?
