[Chimera-users] solvent-accessible area cutoff

[Elaine Meng]

Dear Vamsi,
I do not think there is a definite answer.  This is a somewhat  
philosophical rather than technical question... it depends what you  
are going to do with the resulting list of residues.  You could try  
different values and see whether the resulting set of residues agrees  
with your intuition.

If I remember correctly, there are some alanine scanning papers that  
indicate even residues that are in contact are not always important  
for binding energy.  These were experiments done on protein-protein  
systems, however. Perhaps there are some published papers that discuss  
these issues for substrates -- if anybody has an opinion on this topic  
or can suggest references, please speak up!

However, if you have a protein-ligand complex structure, why not just  
use the "Find Contacts/Clashes" tool instead of dealing with solvent- 
accessible surface areas?   That is what I would use.

"Find Contacts/Clashes" documentation:
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclash.html 
 >

Also, the "distances, H-bonds, contacts" section of this tutorial  
includes an example of finding residues that interact with a ligand:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ 
squalene.html>

Best,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Sep 30, 2009, at 3:33 AM, vamsi krishna wrote:

> Dear all,
>                 I am using chimera to calculate solvent  
> accessibility of residues , may i ask you what cutoff is appropriate  
> to identify surface residues significant for substrate binding .
>
> Thank you
> vamsi