Hanudatta Atreya wrote: > I am trying to model a protein which has 70% sequence similarity to the > template sequence. However, there are ~20 residues in the target/query > sequence which is not present in the template. > > Now, from Secondary Structure Prediction algorithms, this region seems > to be partly helical. But the model generated by Modeller (9v3) gives a > random-coil or loop for these residues. Is it not possible to feed the > secondary structure info. into the program to improve the structural > quality of this extra region?
Yes - you can certainly add secondary structure restraints. Search for it in the manual. It also came up very recently on this mailing list - look in the archives, specifically at http://salilab.org/archives/modeller_usage/2008/msg00040.html
Ben Webb, Modeller Caretaker