From owner-chemistry@ccl.net Wed Nov  9 12:37:00 2005
From: "Elaine Meng meng|,|cgl.ucsf.edu" <owner-chemistry(!)server.ccl.net>
To: CCL
Subject: CCL: Active site volume and surface exposure
Message-Id: <-29911-051109123443-28595-1lXP93zWATjWcqWbiIZ5WA(!)server.ccl.net>
X-Original-From: Elaine Meng <meng!^!cgl.ucsf.edu>
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Date: Wed, 9 Nov 2005 08:57:12 -0800
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Sent to CCL by: Elaine Meng [meng ~ cgl.ucsf.edu]
Hi Kim,
The following papers used an RMS distance of interface atoms to
a least-squares plane (there are many more papers, but these will
get you started):

Jones and Thornton.
Prediction of protein-protein interaction sites using patch analysis.
J Mol Biol. 1997 Sep 12;272(1):133-43.

Chakrabarti and Janin.
Dissecting protein-protein recognition sites.
Proteins. 2002 May 15;47(3):334-43.

Another measure I've seen is length to width to depth:

Preissner, Goede, and Frommel.
Dictionary of interfaces in proteins (DIP).
Data bank of complementary molecular surface patches.
J Mol Biol. 1998 Jul 17;280(3):535-50.

Hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                          meng{=}cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                      http://www.cgl.ucsf.edu/home/meng/index.html

> Sent to CCL by: Kim Branson [kim.branson(~)gmail.com]
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>
> Hi all,
>
> I'm currently looking for a method that can determine the volume of an
> active site and its surface exposure. I'm conducting a validation  
> study
> on protein-protein interaction inhibitors and i would like to quantify
> the oft heard expression "protein-protein interfaces are often flat
> featureless surfaces". I'd like to compare the binding sites to  
> that of
> other systems, and hopefully examine the relationship between scoring
> function performance and active site volume/surface exposure.
>
> I have a crude metric using the ratio of the volume of the active site
> to the total solvent accessible surface of my defined binding  
> region. I
> feel there might be a better way to do this.
>
> cheers
>
> Kim