[Chimera-users] Docking a ligand

Elaine Meng meng at cgl.ucsf.edu
Mon Jan 4 13:48:00 PST 2010

Dear Sriram,
Chimera does not do docking -- it does not predict how structures will  
bind each other.   For docking calculations, you would need to get  
another program such as DOCK:  <http://dock.compbio.ucsf.edu/>

Alternatively, you could try to dock the structures by hand in Chimera  
(move them relative to each other and rotate bonds), but it is  
generally difficult.

However, Chimera includes
(a) a Dock Prep tool for preparing structures before docking
(b) a ViewDock tool for looking at the output from DOCK, and an  
associated tutorial:

Besides the docking calculation, you have another problem -- you need  
a 3D structure for your compound.  If it is something that you can  
find in PubChem
you may be to use "File... Fetch by ID", choose "PubChem" and then  
enter the compound's CID number to get a 3D structure.  This uses a  
web service provided by Chembiogrid at Indiana University.  For  
example, I went to PubChem and searched for "diphenhydramine." I see  
it has the CID 3100, which allows me to fetch the 3D structure into  

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

On Jan 4, 2010, at 12:40 PM, SRIRAM SATAGOPAN wrote:

> Hello,
> I have a receptor molecule (pdb file of the protein) and the  
> chemical formula for the compound that I want to dock it with. I am  
> assuming that I need to use the viewdock program to look at the  
> docking interactions, but I just don't know how to go about it  
> without a structure file for the ligand molecule. Is there a simple  
> way to generate the coordinates for the ligand from the chemical  
> formula? I would appreciate if someone in the group can help me out  
> with this.
> Thanks.
> Sriram

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