regarding flex bb design. As I mentioned before I tried doing fixbb/relax cycles with rosetta3 and am now comparing this to the Rosetta++ mvbb flex backbone design protocol. I am finding that the lr bb-bb hbonds are much better with the Rosetta++ protocol than doing fixbb/relax cycles I was doing with Rosetta3.
So, in conclusion, a good flexible backbone design app in Rosetta 3 would be a great help.
In fact, on closer inspection I was wrong about the above – the energies seem to be worse! So, please ignore.