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Anonymous
SunH, thanks for pointing that out!
Generally, the Rosetta servers (Design, Dock, Robetta (abinitio), FlexPepDock, others) do a great job for a first-pass model of a problem. A local installation of Rosetta running on a supercomputer/cluster will give better results than the servers will because a lot more computing muscle is available. (Actually, RosettaDesign can do complete treatments of most fixed-backbone problems provided the design space is sufficiently small – it’s a tired, wheezy old machine but the fixed-backbone problem is so well treated by Rosetta that even old hardware can handle it.)