[Chimera-users] Fwd: Drug-Protein Interaction

Elaine Meng meng at cgl.ucsf.edu
Mon Feb 18 09:56:21 PST 2013


Hi Kanika,
Take a look at the ViewDock tutorial.  It looks at H-bonds between ligand and receptor using the FindHBond tool.

<http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/tutorials/vdtut.html>
<http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/findhbond/findhbond.html>

Another tool that might be useful for this purpose is Find Clashes/Contacts (in menu under Tools... Surface/Binding Analysis):
<http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/findclash/findclash.html>

I also recommend doing the Structure Analysis and Comparison tutorial, which uses distance measurements, FindHBond, Find Clashes/Contacts etc. to examine a binding pocket:
<http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/tutorials/squalene.html>

I hope this helps,
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 Feb 18, 2013, at 3:34 AM, kanika sharma wrote:
> 
> Hi All,
> I docked a drug to a protein structure using Autodock Vina. To view the result, I am using View Dock. I now have 5 positions in which the drug is docked into the protein. Is there a way to figure out which residues in the protein are interacting with the drug molecule at each position?
> -- 
> Regards,
> Kanika Sharma




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