Hi David, I don't have much experience running AlphaFold 3 predictions. If Google releases the code some day it will be more convenient to run lots of tests. But the AlphaFold 3 paper did talk specifically about how predictions with phosphorylation improved backbone geometry in Extended Data Fig. 6: Analysis and examples for modified proteins and nucleic acids. https://www.nature.com/articles/s41586-024-07487-w/figures/11 Tom
On Jul 30, 2024, at 8:15 AM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi David, Please send questions to the chimerax-users address CC'd here instead of to me individually. I am not an AlphaFold expert, whereas maybe others on the list can answer your questions.
I removed your link because I didn't know if you were willing to share it publicly. If so, please repost to the group (chimerax-users address CC'd here). Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 30, 2024, at 6:26 AM, David S. Fay <DavidFay@uwyo.edu> wrote:
Thanks for that information Elaine. That is my take as well, but I know much less about these things…
On a slightly different note, I really wish there was an alphafold “best practices” tutorial or methods paper. Mainly I’m focused on protein-protein interactions, which is something I think many people are interested in. I gave a talk to my department recently, where I tried to do some of this. But because this isn’t my area, I rather feel like this is a case of the slightly blind leading the even-more blind. Still, I’ve attached a link to a google folder that contains my talk. I’d love to get feedback on this from experts in the field, such as folks at ChimeraX.
And one last question, which you might have an opinion about. Is AF3 any good at predicted changes in structure with amino acid substitutions? I know that AF2 was not, but given that AF3 includes secondary modifications, it would seem like this capability should be improved? Especially if it’s relying less on MSAs. For that matter, do the folks at ChimeraX have an opinion about how AF3 alters structure and interactions based on modifications like phosphorylation?
Thanks,
David
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