[Chimera-users] Docking ligands and protein using Chimera

Elaine Meng meng at cgl.ucsf.edu
Tue Apr 8 09:23:35 PDT 2014


Good morning,
Chimera itself does not do docking.  It has a tool that connects to an AutoDock Vina web service, but it is quite limited: you can only dock ONE ligand molecule per calculation, and only a small number of output positions can be saved (menu: Tools… Surface/Binding Analysis… AutoDock Vina).
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html>

I believe you will need to use some other program outside of Chimera to do the docking.  After that, you can view and analyze the docking results with Chimera (menu: Tools… Surface/Binding Analysis… ViewDock).   
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/viewdock/framevd.html>

What docking program to use?  Possibilities include DOCK, AutoDock, AutoDock Vina, GOLD … there are links to the websites of these programs in the ViewDock manual page linked above.  Some are free for academic use, and downloads and tutorials are available on their websites.   There are also some web servers (so you wouldn't have to download another program), but they may limit your options.  I haven't tried them, but a couple that I know of are:
Dock Blaster <http://blaster.docking.org/>
SwissDock <http://www.swissdock.ch/docking>

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 Apr 8, 2014, at 7:17 AM, Sook Wong <swong18 at terpmail.umd.edu> wrote:

> Good morning,
> I am currently doing research with a professor for protein-ligand structure and would like to dock the receptor molecule (pdb file of the protein) and ligands (pdb file of the sugars). Since I have both the structure files from Chimera, how would I predict and assume which orientation bound to each other forming a stable complex?
> Looking forward to hear from you.
> Thank you so much!
> Sincerely,
> Sook Y Wong
> Chemical and Biomolecular Engineering '14
> A. James Clark School of Engineering
> University of Maryland, College Park, MD 20742 
> swong18 at terpmail.umd.edu




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