CASP14 #s just came out and they’re astounding—DeepMind looks to have solved protein structure prediction. Median GDT_TS went from 68.5 (CASP13) to 92.4!!!! Cf. their 2nd best CASP13 struct scored 92.8 (out of 100). Median RMSD is 2.1Å. I think it's over [0]
and
“I think it’s fair to say this will be very disruptive to the protein-structure-prediction field. I suspect many will leave the field as the core problem has arguably been solved,” he says. “It’s a breakthrough of the first order, certainly one of the most significant scientific results of my lifetime.” [1]
I can't square this with the actual competition results. There are tons of targets where AlphaFold2 didn't score over 70%. It was typically only 10% ahead of the next best program. The metric everyone is looking at, GDT_TS, gives marks for atoms that are within eight angstroms of where they should be - by experimental standards, eight angstroms is a huge miss! There are targets where on some important metrics, like C-alpha RMSD, AlphaFold2 did worse than another program!
You're making extremely strong claims, counter to scientists with no incentive to praise Google being quoted with reactions such as expecting a mass exodus from computational biology. I, and I assume we, are open to hearing more but I'm not sure cherry-picking a couple examples is enough to credit your claims contra theirs.
For instance, the gentlemen who was presented as a skeptic is instead shown to also say it's solved, and in reply to this you say "everyone" is looking at the "wrong" metric, and it allows errors of 8+ atom widths - he notes the median error is 2.1 angstroms, or 2.1 atom widths.
I feel like there's a certain je ne sais quoi to the comments Google employees write where I can just immediately sense them without even needing to check.
Here is what Mohammed AlQuraishi said in 2020:
CASP14 #s just came out and they’re astounding—DeepMind looks to have solved protein structure prediction. Median GDT_TS went from 68.5 (CASP13) to 92.4!!!! Cf. their 2nd best CASP13 struct scored 92.8 (out of 100). Median RMSD is 2.1Å. I think it's over [0]
and
“I think it’s fair to say this will be very disruptive to the protein-structure-prediction field. I suspect many will leave the field as the core problem has arguably been solved,” he says. “It’s a breakthrough of the first order, certainly one of the most significant scientific results of my lifetime.” [1]
[0] https://twitter.com/MoAlQuraishi/status/1333383634649313280
[1] https://www.nature.com/articles/d41586-020-03348-4