Modelling extra residues, not present in template
Dear all,
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?
Thanks Regards Hanudatta
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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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Hanudatta Atreya -
Modeller Caretaker