[chimerax-users] Superimposition with chimeraX

[Elaine Meng]

Hello Hyunsook,
ChimeraX does not predict how chemicals bind to proteins.  The positioning of the structures relative to each other when you simply open them is not meaningful.

To predict the binding location you need to use some other program.  There are many programs for molecular docking (to do this type of prediction):  DOCK, Autodock Vina, Swissdock, Glide, and many others.

Then, after you use another program for docking and get an output file, you may be able to view and analyze the output in Chimera or ChimeraX.  Currently Chimera knows more docking-output formats than ChimeraX does.

Docking programs:
DOCK <https://dock.compbio.ucsf.edu/index.html>
Autodock Vina <https://vina.scripps.edu/>
Swissdock web server <http://www.swissdock.ch/>  (includes video for how to view output in Chimera)
Glide <https://www.schrodinger.com/products/glide>

Chimera ViewDock tool for looking at docking output:
<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/viewdock/framevd.html>

Chimera ViewDockX tool for looking at docking output:
<https://rbvi.ucsf.edu/chimerax/docs/user/tools/viewdockx.html>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Mar 18, 2022, at 11:00 PM, 이현숙 via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Hello.
> I would like to superimpose chemical structure to protein structure.
> Protein structure was created by tool - structure predict - alphafold.
> Chemical structure was added to the protein structure( via tool - structure edit - add smile string - build structure)
> My question is :
> when chemical structure is added on the protein structure, chemical structure is located at the active site OR just located at the center of protein structure ?
> I want the 1st one (located at the active site) then how can I do through ChimeraX?
> 
> Thank you.
> Hyunsook 
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