[Chimera-users] Enquiry docking

Thuluz thuluz at gmail.com
Tue Nov 20 14:16:57 PST 2018

Dear Elaine C. Meng,

It is quite true! Thanks a lot anyway

Thanks I will direct the message to the Scripps people.

kindest regards


On Tue, 20 Nov 2018 at 16:09, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> 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):
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html>
> … 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.
> Best,
> Elaine
> -----
> 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

*Dr. Thuluz Meza Menchaca*
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