Hi Denis,
I have inserted my comments in your text:
Modeller Caretaker wrote:
Forwarding to list.
----- Forwarded message from Denis Volkov <> -----
Date: Thu, 11 Sep 2003 14:15:18 +0400
From: Denis Volkov <>
X-Mailer: The Bat! (v1.52f)
Organization: IBCH
To:
Subject: Re: model_refinement
Hello,Oliver
Thank you for fast answering! :)
No i didn't test a quality of templates course i
used 4 structures
as a templates so its difficult to do it.
You can run procheck on all 4 templates to get a feeling for the best
quality you can expect from your model. Why not?
How did you check the alignment. My experience is that, if the sequence
alignment suggests an alignment of a segment of the target sequence
with all templates, it is important that the template structures are
really very similar for this segment. I.e. you need to check the
alignment on basis of the superposed template structures.
Alignment
I manually adjust
so it's not a origin of fault. I look at the model
again and think
it's not so bad as I said. But a problem is more
global:
A similarity with templates is no more than 20%. A
great deal of
mismatches are in loop origin so it's not so
bad...but can i do a good
model with so low similarity? As I said I use
Charmm, I used it to investigate
protein-protein interactions. I used Modeller model
to investigate
enzyme-substrate and enzyme-inhibitor interaction.
But after MD a
structure was a great deal disturbed. Is it a
problem of low
similarity or as you said its not good to use MD
with models maid by
Modeller?
I would not expect too much of a model based on sequence identity with
the templates in the range of 20 percent. Did you do the MD without any
restraints? You could apply restraints on the regions of your model
which you expect to be correct based on the alignment - in case this
makes any sense with respect to the problem you are investigating. I
would not expect a stable MD without restraints for a model on basis of
20% identity with the templates. But this actually is only my guess. In
general one can usually not expect a homology model to get closer to the
actual (experimental) structure by doing a MD simulation (see Proteins
48 (4): 593-604 SEP 1 2002).
Best,
Oliver
____________________________________________________________
Oliver Hucke (PostDoc)
Biomolecular Structure Center
Dept. of Biochemistry
University of Washington
Health Sciences Building K-418C