[Chimera-users] Conformation Search in Chimera

[Elaine Meng]

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
>