[Chimera-users] Making oligomers from Alphafold predictions

[Elaine Meng]

Hi Smith,
The latest ChimeraX daily builds (not the production release) include getting AlphaFold-predicted structures from the freely available AlphaFold Database.

However, these are single-chain predictions only.  There is an option to superimpose the single-chain predictions on an experimentally determined structure of a multimer so that the result looks like a multimer, but that is not truly the same as predicting the multimer.

AlphaFold Database:
<https://alphafold.ebi.ac.uk/>

ChimeraX AlphaFold tool and command:
<https://rbvi.ucsf.edu/chimerax/docs/user/tools/alphafold.html>
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/alphafold.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 Aug 31, 2021, at 4:28 AM, tim smith via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Hi All,
> Apologies for the nonrelated question!!
> 
> Wondering if there are any tools (can make in chimera/chimerax/Pymol) that predict or build protein oligomers based on alphfold structure.   Please let me know. I will be grateful for your kind responses. Thank you 
> 
> Best
> Smith