Subject: [modeller_usage] Questions on loop modelling
From: hori koshii <>
Date: Fri, 16 Jun 2006 13:06:07 -0700 (PDT)
My target sequence has two insertions at 2 loop regions (14aa, 9aa) when compare to my template structure. I have three questions:
1. Since 12aa is the limit of loop modelling, is that viable to build a "model" with the "template sequence plus 2 aa of the "target" insertion, then use this "template +2aa" model as template for building the model of the target????
2. The residues flanking the insertions also belong to the loop regions (of the template), so, my question is, when we do loop modelling, do we need to model the whole piece of loop for accuracy??
3. When we generate loop models, do you model one loop and then the other? Since I have two loop regions, I wonder if I should build (~500) models for one regions and then another set for the other region? Does one loop region actually affect the conformation of the other loop? Do you think it's necessary to build them both at the same time?
Thank you very much for answering the
questions. Have a great day.