Generally speak the peptide docking is much more chalenged than protein-protein docking for the peptide backbone is much more flexible than protein. Because of this reason, many peptide docking tools would introduce annealing and solvent model. I am wondering, does Rosetta also good at such kind of work?
If I want to do a peptide docking, may I also use solvent model(such as TIP3 and so on) and annealing during the docking?
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.)