[ccp4bb] Judging a homology model

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

Previous message:
Subject: Re: PDB Validation Report
From: Jasmine Young jasmin {- at -} RCSB {- dot -} RUTGERS {- dot -} EDU
Date: 2010-01-05

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

Subject: Judging a homology model
From: Raja Dey deyraja1 {- at -} YAHOO {- dot -} CO {- dot -} IN
Date: 2010-01-05

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 answerâ€¦
Happy New Year to you all,
Raja

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CCP4bb navigation

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

Previous message:
Subject: Re: PDB Validation Report
From: Jasmine Young jasmin {- at -} RCSB {- dot -} RUTGERS {- dot -} EDU
Date: 2010-01-05

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