CCL: Active site volume and surface exposure

 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