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Re: [ccp4bb] Judging a homology model
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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999
Previous message:
Subject: Judging a homology model
From: Raja Dey deyraja1 {- at -} YAHOO {- dot -} CO {- dot -} IN
Date: 2010-01-05		Next message:
Subject: Re: Judging a homology model
From: Jürgen_Bosch jubosch {- at -} JHSPH {- dot -} EDU
Date: 2010-01-05


Subject: Re: Judging a homology model
From: Nathaniel Echols nathaniel {- dot -} echols {- at -} GMAIL {- dot -} COM
Date: 2010-01-05

On Tue, Jan 5, 2010 at 9:24 AM, Raja Dey wrote:

> Assuming all the above data are right, which of the following way would
> give the best model for C?
>
> 1. Building homology model of C with A as template.
>
> 2. Building homology model of B with A as template and then use B as
> template to build C.
>
> Suppose I used MODELLER for this work where an energy minimization step is
> involved after threading the query sequence on the template.
>
> I need to know which model for C will be better and why?
>
(1). I don't have time to list all of the reasons, but it is a certainty
that the dissimilar residues between A and B are not all in the same
positions as the dissimilar residues in B and C, and each dissimilar residue
is going to result in a less accurate model - so if you model A->B->C, you
will be propagating errors. (There is probably a formal mathematical way to
express this - there have been many studies on sequence similarity vs.
RMSD.) If you need to convince yourself further, find three structures with
similar sequence identities in the PDB, run the experiment with them, and
compare the end result to the actual structures.
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