I have a 11aa long linker (known sequence) connecting two parts of a protein (NOT two independent domains). I want to model the linker before some downstream Rosetta analysis on the protein. It seems FloppyTail is often suggested for the modeling of linkers.
My question is: how is FloppyTail compared to Remodel + Fixbb? What if I just insert some 11aa long extension (of any sequence) between the two parts using Remodel, then I use fixbb to mutate this newly inserted extension to the sequence of my linker? How would this compare to FloppyTail?
You say your two domains are not independent – how are they related?
If they’re attached in a known fashion – they have a known interface – then you have an 11 residue loop, not a linker, and you should use loop modeling. If the problem is that your two domains have a known structure, but the 11 residues are missing, then remodel->fixbb->loop modeling is an appropriate way to get those residues in. You can also just skip the first two steps by editing the PDB file manually.
If you do not know how the domains interact, then you have a linker, and FloppyTail is reasonable. Remodel is probably reasonable too (but I haven’t used it, so I can’t say much about it).
If you are using FloppyTail between domains, it is going to move those domains relative to one another – essentially it is going to sample their docking interface by moving the linker between them. This is inefficient but sometimes the best way to approach the problem. Sometimes it is better to just do docking, get an interface, then solve the loop with loop modeling instead.