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
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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/
