I'm a newbie at Rosetta, and I need to figure out if i can do something.
I have an assymetric homo dimer PDB structure, but each monomer has about ~230 missing residues (with predicted high probability of being disordered). Each monomer has this organization (from amino to carboxyl):
[known structure domain][missing structure domain]
The protein-protein interactions of the asymm dimer are between the domains with known structure. I need to figure out how the missing structure domains interact with the structured ones, through the generation of thousands of models.
At a monomer level, I was thinking about modelling the complete sequence by ab initio. Then, using as templates the PDB of the known structured domain plus the structure of the ab initio modelled missing region execute a comparative modelling to obtain the complete monomer structure.
The question is, is there a better way to make a mix of ab initio plus comparative modelling?
is it posibble to implement this modelling at assymetric dimer level? specially considering that the missing structure domain of one monomer perhaps may interacts with the other monomer.
Any help or suggestions are greatly appreciated!!