Again, it's entirely possible I missed some very subtle point in AF2's system, but my understanding is that each target AF2 predicted had an underlying structural template covering the majority of the domain and the mapping was established through the MSA.

IE, any MSAs would always include alignments to known protein structures. Are you saying their MSAs don't include alignments to known protein structures?

(the reason I'm asking all this is because if I'm mistaken, then AF2 did do something "interesting", but everything in the paper says that everything they did is template based. If they are just folding proteins using MSAs without alignments to protein structures, that's far more interesting. I don't think they did that.

edit: I've now reread the paper again, and I believe their claim of making predictions where there is no structural homology is incorrect from a technical perspective. I've communicated this to both the CASP organizers (whom I know) and DeepMind.