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?