[Chimera-users] solvent-accessible area cutoff
meng at cgl.ucsf.edu
Wed Sep 30 08:53:45 PDT 2009
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:
Also, the "distances, H-bonds, contacts" section of this tutorial
includes an example of finding residues that interact with a ligand:
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
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