I am new to rosetta, so can someone help me to figure out how to do ab-initio for a subunit in a multimeric protein.
I am interested in doing ab-initio for one subunit whose crystal structure is not known and the crystal structures of other non-covalently interacting subunits are completely known. It is experimentally known that the subunit whose crystal structure is not known is predominantly helix and also the approximate position of the helix is also known.
If you were trying to fold a symmetric homo-oligomer, there’s the application FoldAndDock, but that’s not for heteroligomers, though.
I am not aware of a protocol in Rosetta which will ab-initio fold a protein in complex with another protein (even one where the interacting partner is already know). What I would suggest to try instead is to do a regular ab inito run with the unknown protein, and then in addition to the regular post processing, do protein-protein docking runs with the putative models (probably limited to cluster centers, to keep the computational costs down). Hopefully, one of the clusters will stand out as having a good docking energy. You can then further explore members of that cluster to see which model best balances folded structure and binding energy.