[Chimera-users] Enquiry docking

Elaine Meng meng at cgl.ucsf.edu
Tue Nov 20 14:09:18 PST 2018

Dear Dr. Thuluz Meza Menchaca,
The docking is not done inside Chimera.  As explained in the page describing the “Autodock Vina” tool in Chimera (you can also see this by pressing the Help button on the dialog):

… the structures are sent to a web service run by another lab (NBCR), where it executes a program named “Autodock Vina” that is developed by another lab (at Scripps) and then when the results come back, Chimera automatically shows them.

I am not an expert on how this docking program works.  To understand it, you can read the reference given in the help page for which I gave the link above.

As far as I know, there is no special reason why the center of the box would be any more likely than other parts of the box.  The results are just what gives the best interaction score with the protein, out of the positions that are sampled.  Also if you mean that you are getting different results with the same molecules, the web service does not allow very much sampling, so it is not surprising if different runs do not converge to the same result.

If you want to do a high amount of sampling, you may need to get the Autodock Vina software yourself from the Scripps website (also linked to the help page above), install it on your computer, and run it directly  (not using Chimera). However, that would require learning how to use Autodock Vina directly.
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Nov 20, 2018, at 9:43 AM, Thuluz <thuluz at gmail.com> wrote:
> Dear Chimera users and technical assistance, 
> I would like to ask you about molecular docking issue. We are performing a number of blind dockings, always by posing the grid box at the centre of a given molecule, the box had always the same size.
> Our question is why sometimes we get docking results very close to the centre and sometimes further away from it? is it only random or depends on physic-chemical properties?
> thanks in advance for any help on this matter,
> my best regards
> -- 
> Dr. Thuluz Meza Menchaca

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