Comment by CuriousEcho on I'm a bit skeptical of AlphaFold 3 · 2024-06-26T01:20:11.194Z · LW · GW

Since this shows up in homomeric proteins, maybe the issue is because symmetry breaking in quartinary structure happens late in training. This is just a guess tho... but aligns with my intuitions on training dynamics. I would also guess that this would get ironed out in the tails of the loss curve, if we push out further in training. I think the PLDDT loss would first learn to stack homomers on top of one another and then spread them out. I haven't used alphafold too much but the smoking gun plot id be interested in is clashes in heteromers vs clashes in homomers. It's a curious little detail, thanks for sharing this finding!