Excuse this if it has arrived twice. Greetings
Just done an NMR structure of a protein that can form a hexamer. I'd basically like to model/generate the hexamer using the NMR structure of the monomer. There is a protein with good sequence identity (45%) that is a heptamer, to model the likely interfaces. I think it may be possible to use Marius' RGyr term/Rigid body docking methods to assemble the hexamer using partial ridgid bodies, floppy sidechains etc and to include a couple of loose synthetic NOEs) along with crystalography symmetry terms. Is the best way to do this to first build up 3 dimers using the RGyr/NOEs (they will not be symmetric, head-tail) then asemble the hexamer from dimer1->dimer2 then dimer1-dimer-2->dimer3?? But can I define several different radius of gyration terms? or 3 or even 6 and use crystalographic symmetry. i.e. do the lot at once? Has anybody done this kinda thing? Is there an obviously easy easy way that I've missed? I can model a hexamer rather than the heptamer on something else but the interface may not be as good as the sequence identity is much lower. then I can do the 6 RGy + some NOE from the heptamer etc.... thanks James
