Subject: Re: [modeller_usage] regarding N terminus region
From: Modeller Caretaker <>
Date: Wed, 17 Oct 2007 10:22:06 -0700
Cc: modeller_usage <>
simran jeet wrote:
I have a protein sequence whose N terminus region does not matches with
the template. Is it neccessary that N and C terminus regions of a
protein should be fixed for homology modeling? The n terminus region
contains 12 residues. There are long gaps also within the
alignment. Can these regions be modelled by loop modelling? I am also
attaching the alignment file.
You can certainly try to build a model without a template for the N or C
termini, but what you'll probably find is that you'll just get very
flexible regions with no secondary structure, so you're probably better
off removing those regions from your target sequence. Gaps within your
sequence up to about 8-12 residues should be amenable to loop modeling,
providing you build enough models to get reasonable sampling.