As a part of my work I have to redesign and exchange the loops of target protein with other loops (irrespective of the length) after going through some literature I have found that Fixed backbone design could help in redesigning the loops with desired residues but I couldn't find any method regarding loop exchange, Could any one tell me is there any reliable protocol to do loop exchange in Rosetta and also I would like to know whether my choice of fixed backbone design to redesign loops is a correct one. Please ignore my layman knowledge as I am new to Rosetta.
A) Fixed backbone design is, in a literal sense, your only option for design. Even flexible backbone design protocols are just doing design on snapshots of fixed backbone, by iterating between backbone remodeling and loop remodeling.
B) I don't think we have an executable that does loop design as-is; the primary loop modeling executable historically won't do design. You can do it with RosettaScripts.
C) If you mean "loop exchange" as in, you have proteins A and B and want to put the loops from A onto B, including their conformations, there is not executable for that; just use a combination of PyMOL + emacs + CCD-style loop closure through the loop modeling executable to get close.
D) If you mean "loop exchange" as in, put the sequence of loop B onto the structure of loop A and then remodel loop A to see what it looks like in its new protein/sequence context, that is best done with fixbb (to fix the sequence) followed by loop remodeling. There is a demo somewhere for adding/removing loops from residues manually if this is what you want to do.
E) If you mean general "loop exchange" as in, replace the loops of protein A with lots of different loops from anyplace else in the PDB, that is the loophash protocol (http://onlinelibrary.wiley.com/doi/10.1002/jcc.23069/full) which we haven't released yet.
Thank you for the information, I'll post back if had any problems.