[chimerax-users] ChimeraX for multimeric prediction

[Elaine Meng]

Greetings Abdul-Vehab,
We're glad you like ChimeraX!

As for your question: sorry no, ChimeraX does not include multimer prediction, other than the interface to running AlphaFold-Multimer.  

Any reliability measures on the predicted multimer from such a calculation come from AlphaFold itself:

(A) the individual residue (pLDDT) values shown with coloring 
<https://rbvi.ucsf.edu/chimerax/docs/user/tools/alphafold.html#coloring>
<https://alphafold.ebi.ac.uk/faq#faq-5>

(B) the residue-residue "predicted aligned error" as shown in the PAE plot
<https://rbvi.ucsf.edu/chimerax/docs/user/tools/alphafold.html#pae>

... or with colored lines using command "alphafold contacts"
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/alphafold.html#contacts>

There are lots of other programs for protein-protein docking (maybe google it), but ChimeraX does not have an interface for running them, although of course ChimeraX could be used to view the results.

ChimeraX has general tools that may help give clues, such as showing a hydrophobic patch on the surface (e.g. command "mlp") but they would not in themselves predict a specific multimer or its configuration.

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


> On Sep 30, 2022, at 10:37 PM, Dozic,Abdul-Vehab via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Greetings,
> Firstly, I wanted to say that ChimeraX is excellent software, and it can definitely be helpful to enhance our research experience. I wanted to ask about using ChimeraX to predict whether a protein occurs in a multimeric form. I ran Alphafold for multimeric simulations and I have analyzed the predicted aligned error qualitatively, but I was wondering if ChimeraX had some built-in package for fast error analysis such as that it can tell us automatically whether it is likely to find a protein in a particular multimeric state that was modeled by Alphafold. 
> Thanks,
> Best,
> Abdul-Vehab