[Chimera-users] Conformation Search in Chimera

[Maj Krumberger]

Hello Dr. Meng,

Thank you for letting me know!

Best,

Maj Krumberger

Graduate Student - Nowick Group
Department of Chemistry
maj.krumberger at uci.edu



University of California, Irvine
4302 Natural Sciences I
Irvine, CA 92697-2025


On Wed, May 6, 2020 at 12:59 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hello Maj,
> Sorry no, there is no such conformational search tool in Chimera.
>
> I'm not an AutoDock Vina expert, but I believe that it can include ligand
> flexibility, so it may be unnecessary to input multiple conformations.
> You'd need to check its documentation:
> <http://vina.scripps.edu/>
> Also the lowest-energy conformation of some flexible ligand by itself is
> unlikely to be the same as the lowest-energy conformation in the context of
> the binding site.
>
> I don't know if you were planning to use the AutoDock Vina tool in
> Chimera, but if so, you should be aware that the web service it used is no
> longer available.  To use that tool now requires installing AutoDock Vina
> on your own system, which may not be practical for a class. I've updated
> the help page to say all that:
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html>
>
> There are various other docking servers, but you would have to use them
> separately, not from Chimera.  Some of those web servers provide a results
> file that you can open  and view using the Chimera ViewDock tool. I don't
> have a specific recommendation, but a couple of examples are:
>
> Webina
> <https://durrantlab.pitt.edu/webina/>
> <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2020-April/016764.html>
>
> Swissdock
> <http://www.swissdock.ch/>
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
>
> > On May 6, 2020, at 11:23 AM, Maj Krumberger <mkrumber at uci.edu> wrote:
> >
> > Hello,
> > We are currently developing an educational exercise in Chimera for
> building different inhibitors in different proteases, using Chimera and
> then using AutoDock Vina for finding potential docking sites. I was
> wondering if there is a function in Chimera for doing a conformational
> search that we could do  to find the lowest energy conformer before running
> AutoDock Vina?
> >
> > Thank you,
> > Maj Krumberger
> >
>
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