Re: [modeller_usage] Modeling large protein sequence having homologues with less similarity.
To: Sehrish Batool <>
Subject: Re: [modeller_usage] Modeling large protein sequence having homologues with less similarity.
From: Modeller Caretaker <>
Date: Mon, 06 Jul 2009 14:41:46 -0700
On 07/06/2009 12:27 AM, Sehrish Batool wrote:
My target sequence of protein is too large containing more than 1000
amino acids and I found 4 homologues in PDB showing very less similarity
i-e. two showing 28% similarity, one showing 24% and last one showing
19% similarity with my target sequence.
Depending on your alignment method and the fold assignment, that may be OK.
Also the starting residues of
templates have no homology with my target sequence and Modeller has to
read from 1st residue of template, that bocomes impossible in this case.
I don't know where you got that idea from - Modeller does not have to
read from the first residue of each template. You can read any
contiguous range (if the range is not contiguous you can simply edit the
PDB file so that it is, or just don't align the unwanted template
residues with your target sequence).