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

[Modeller Caretaker <modeller-care@ucsf.edu>]

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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