From owner-chemistry.,at,.ccl.net Fri Mar 30 14:35:00 2012
From: "Arun Kumar Subramanian aksub007=-=gmail.com" <owner-chemistry__server.ccl.net>
To: CCL
Subject: CCL: how much homology models could be trusted for looking at the dynamic comparisons.
Message-Id: <-46601-120330140016-19120-i/kfCa5cD/vluDe5p8mvbw__server.ccl.net>
X-Original-From: Arun Kumar Subramanian <aksub007%gmail.com>
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Date: Fri, 30 Mar 2012 23:29:45 +0530
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Sent to CCL by: Arun Kumar Subramanian [aksub007],[gmail.com]
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Dear CCL Users,
I am trying to see if homology model of a GPCR could be trusted in order to
compare the low frequency motions with other homologous proteins for which
crystal structures are available. The template sequence has 37% similarity
and hence I thought of proceeding further because most (almost all) of the
reported homology models of GPCR are only around this value. I would guess,
if any bias should show up, it should stem out from the fact that the fold
is simply borrowed from the template and/or the differences in side chain
orientations. I am thinking of reducing this bias via unrestricted,
explicitly solvated MD simulations using the built homology models or with
back bone restrictions, for around 2-3 ns or upto 5 ns, such that the side
chain orientations could be treated in a better manner. Then, I plan to
compare those with the crystal structures on the properties of their
collective motions or the low frequency movements. Any suggestions if this
will work out? or any experience in similar lines? welcome to share with me.

Thanks.

Sincerely,




ArunKumar. S.

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<h3 class="groups title">Dear CCL Users,<br></h3>
                      I am trying to see if homology 
model of a GPCR could be trusted in order to compare the low frequency motions with other 
homologous proteins for which crystal structures are available. The template sequence has 37% similarity and hence I thought of proceeding further because most (almost all) of the reported homology models of GPCR are only around this value. I would 
guess, if any bias should show up, it should stem out from the fact that
 the fold is simply borrowed from the template and/or the differences in side chain orientations. I am thinking of 
reducing this bias via unrestricted, explicitly solvated MD simulations 
using the built homology models or with back bone restrictions, for around 2-3 ns or upto 5 ns, 
such that the side chain orientations could be treated in a better 
manner. Then, I plan to compare those with the crystal structures on the
 properties of their collective motions or the low frequency movements. 
Any suggestions if this will work out? or any experience in similar 
lines? welcome to share with me.<br><br>Thanks.<br><br>Sincerely,<br><br><br><br><br>ArunKumar. S.<br>

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