I am new to using Alphafold 2 and have been primarily using ChimeraX and Colabfold to run some preliminary predictions. I am particularly interested in using AF2 to predict the homo-oligomerization number of a protein. I have attempted this initially by manually running several predictions with different multiples of the protein end to end ("ABCD:ABCD"). This works but does not provide any direct comparison of plausibility between different oligomerization possibilities, and does not establish a firm prediction as to what the oligomerization state of the protein is.
I have read a paper (https://doi.org/10.1038/s41594-022-00849-w) which appears to use Alphafold2 to make predictions about oligomer count. These researchers appear to use Colabfold for at least part of this calculation.
Can Alphafold 2 (and Colabfold in particular) be used to make predictions about homo-oligomeric state in this way? If so, how?
Thank you.
