Re: [modeller_usage] How to deal with a part of protein sequence that have no alignment with the template
To: xiazhendong1986 <>
Subject: Re: [modeller_usage] How to deal with a part of protein sequence that have no alignment with the template
From: Modeller Caretaker <>
Date: Tue, 29 Sep 2009 09:10:15 +0100
Cc: modeller_usage <>
xiazhendong1986 wrote:
...
As we can see from above, the templates have no sequence from amino 1 to
70 to align with the target protein "sldha", and the modelling result is
that the structure of sequence 1-70 is a just a long chain with no fold.
So how can I get the structure of sequence 1-70?
Modeller is a package for comparative modeling, so if you don't have a
template,
it won't be able to generate a reasonable-looking model. You may be able
to find
another template that aligns reasonably well with that range, for example by
using a more sensitive search for templates such as profile-profile.
If you can't find a template for residues 1-70, you have no option with
Modeller