modeling of higher-order oligomers question about alphapulldown HOT 6 CLOSED

Hi,

Sorry what kind of oligomers would you like to model? Hetero-oligomer or homo-oligomer? If it's a homo-oligomer, then homo-oligomer mode would be suitable and easy to use. If it's hetero-oligomer, then I agree with you that custom mode suits better.

Hope it helps.

Yours
Dingquan

from alphapulldown.

Hi Dingquan,
thank you, yes this would be hetero-oligomers. The paper just sounded as if there is a function that allows automated modeling of combinations of subunits within a complex. Similar to MoLPC. But I think I misunderstood, that the input has to be precisely defined?

from alphapulldown.

Hi,

in the same vein, I would love to be able to make a pulldown not only with single proteins, but with previously calculated multimers (in my case a 1-1-2 heterotetramer).

Certainly a heterotretramer will open up other interaction platforms as a monomer and this is surely happening in "reality"

Is there currently any way to do this? Costum mode has a rather stringent AA cut off.

Thanks!

from alphapulldown.

Hi,

Yes, this is a common request and we're working on it. But it would likely still have same "AA cut off" as AlphaFold.

Best,
Jan

from alphapulldown.

Hi Jan,

thanks for the info - I'll make sure to check back regularily!

Best
Lukas

from alphapulldown.

Hi @DillyOh!
This can be done using multimeric templates and the TrueMultimer mode. Please refer to the documentation for the details:
https://github.com/KosinskiLab/AlphaPulldown?tab=readme-ov-file#14-run-with-custom-templates-truemultimer
https://github.com/KosinskiLab/AlphaPulldown?tab=readme-ov-file#25-run-with-custom-templates-truemultimer

from alphapulldown.