“Also I want to ask that if we already have a database of fragments and I reorder it according to the 9 mer format of rosetta library would it be possible to use it .. and if yes how ??”
I don’t quite understand the question. If you already have fragments, then I’m sure you can transform them from one format to another to get rosetta to like them. I don’t know how to do it, and I’m not aware of any fragment-converting scripts out there, I guess you’ll have to writeone.
“I didnot understand the first part of ur last question… I don’t want any loop designing … What I want is to pick a fragment from a fragment library of say 10 residues and model the loop for the defined region and gives the model without any much structural changes to the backbone of the protein … Since after getting the best model I have to test it in wet lab whether the protein is active or not after the new loop insertion ??”
If you are not designing, then what is there to test? Fragment insertion is generally constant-sequence, and if you don’t change the sequence then what is there to test in the wet lab?
Do you mean, you want to insert the fragment’s sequence along with the fragment itself? That is possible with the newer fragment code in 3.2, but an application to do it that way has never been written. The loop modeling executeable won’t do it. There’s code in development that shows it is possible, but we don’t expect it to be finished for another year or so.
The most recent Rosetta code reference came out last month (you should be able to figure out which author is me!)
Methods Enzymol. 2011;487:545-74.
ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules.
Leaver-Fay A, Tyka M, Lewis SM, Lange OF, Thompson J, Jacak R, Kaufman K, Renfrew PD, Smith CA, Sheffler W, Davis IW, Cooper S, Treuille A, Mandell DJ, Richter F, Ban YE, Fleishman SJ, Corn JE, Kim DE, Lyskov S, Berrondo M, Mentzer S, Popović Z, Havranek JJ, Karanicolas J, Das R, Meiler J, Kortemme T, Gray JJ, Kuhlman B, Baker D, Bradley P.
One of the more recent reviews will cover most of the older reviews:
Biochemistry. 2010 Apr 13;49(14):2987-98.
Practically useful: what the Rosetta protein modeling suite can do for you.
Kaufmann KW, Lemmon GH, Deluca SL, Sheehan JH, Meiler J.