Re: [ccp4bb] Judging a homology model

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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

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From: "Clayton, Gina Martyn" gina_clayton {- at -} MERCK {- dot -} COM
Date: 2010-01-05

Subject: Re: Judging a homology model
From: Jürgen_Bosch jubosch {- at -} JHSPH {- dot -} EDU
Date: 2010-01-05

Hi Raja,

1) how big is your protein ?
2) multiple domains ? What's the ID/sim between domains ?
3) Check Xtalpred in case you've overlooked a closer homolog
http://ffas.burnham.org/XtalPred-cgi/xtal.pl

I would not try to predict an intermediate model and then use that to
predict the final model.

Jürgen

On Jan 5, 2010, at 12:24 PM, Raja Dey wrote:

> Dear Friends,
>
> I have a question about judging a homology
> model. I have three homologous proteins A, B and C of which only A
> has 3D crystal structure available. Their similarities/identities
> are given below.
>
> Pair-wise alignment similarity/identity (%)
>
> A and B 63/49
>
> A and C 54/39
>
> B and C 60/46
>
> 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?
>
> Thanks for your answer…
>
> Happy New Year to you all,
>
> Raja
>
>
>
>
>
> The INTERNET now has a personality. YOURS! See your Yahoo! Homepage.

-
Jürgen Bosch
Johns Hopkins Bloomberg School of Public Health
Department of Biochemistry & Molecular Biology
Johns Hopkins Malaria Research Institute
615 North Wolfe Street, W8708
Baltimore, MD 21205
Phone: +1-410-614-4742
Lab: +1-410-614-4894
Fax: +1-410-955-3655
http://web.mac.com/bosch_lab/

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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

Next message:
Subject: Anions in protein structures
From: "Clayton, Gina Martyn" gina_clayton {- at -} MERCK {- dot -} COM
Date: 2010-01-05