[Chimera-users] Docking a ligand

[Elaine Meng]

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

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
<http://pubchem.ncbi.nlm.nih.gov/>
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  
Chimera.

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 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
>