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Re: [modeller_usage] Modelling extra residues, not present in template

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
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