[Chimera-users] Residues that interact with active site

[Elaine Meng]

Hello Abeer,
If there is some ligand bound or modeled into the site, you can  
certainly use Chimera to identify the residues that contact the  
ligand and/or form H-bonds with it.  This is done, for example, in  
the Structure Analysis and Comparison tutorial using the "Find  
Clashes/Contacts" and "FindHBond" tools:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ 
squalene.html>
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findclash/ 
findclash.html>
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/ 
findhbond.html>

If you only have the protein and no knowledge of where the active  
site is, however, Chimera does not predict the location of the active  
site.  There are many, many Web servers that try to predict active  
sites or important residues given a structure, but I do not have a  
list of these, sorry.

A couple of relevant Web servers that have a connection to Chimera are:

(1) CASTp - finds pockets, often the largest is the active site
(if you get results e-mailed to you, you can view them in Chimera)
<http://sts.bioengr.uic.edu/castp/calculation.php>
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/castp.html>

(2) ConSurf - finds related sequences, makes sequence alignment,  
shows residue conservation by coloring the structure; often the  
highly conserved residues are functionally important (one option is  
to show results in Chimera)
<http://consurf.tau.ac.il/>
<http://www.cgl.ucsf.edu/chimera/consurf/consurf.html>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                       http://www.cgl.ucsf.edu/home/meng/index.html

On Jun 3, 2009, at 3:56 AM, Abeer Shokeer wrote:

> Hello
> I have a model structure of my protein and I would like to determine
> which residues that could take part in active site. Can I do that with
> Chimera?
> Thanks for your help
> Abeer