[modeller_usage] Modelling extra residues, not present in template
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Subject: [modeller_usage] Modelling extra residues, not present in template
From: Hanudatta Atreya <>
Date: Sat, 15 Mar 2008 05:37:06 -0700 (PDT)
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?