zlacker

>>ChrisA+(OP)
AlphaFold is optimization, not thinking. Propaganda 'r us.

>>DrierC+R1
Not sure why this is downvoted. The comment cuts to the core of the "Intelligence vs. Curve-Fitting" debate. From my humble perspective as a PhD in the molecular biology /biophysics field you are fundamentally correct: AlphaFold is optimization (curve-fitting), not thinking. But calling it "propaganda" might be a slight oversimplification of why that optimization is useful. If you ask AlphaFold to predict a protein that violates the laws of physics (e.g. a designed sequence with impossible steric clashes), it will sometimes still confidently predict a folded structure because it is optimizing for "looking like a protein", not for "obeying physics". The "Propaganda" label likely comes from DeepMind's marketing, which uses words like "Solved"; instead, DeepMind found a way to bypass the protein folding problem.

>>Rochus+xj
If there's one thing I wish DeepMind did less of, it's conflating the protein folding problem with static structure prediction. The former is a grand challenge problem that remains 'unsolved' while the latter is an impressive achievment that really is optimization using a huge collection of prior knowledge. I've told John Moult, the organizer of CASP this (I used to "compete" in these things), and I think most people know he's overstating the significance of static structure prediction.

Also, solving the protein folding problem (or getting to 100% accuracy on structure prediction) would not really move the needle in terms of curing diseases. These sorts of simplifications are great if you're trying to inspire students into a field of science, but get in the way when you are actually trying to rationally allocate a research budget for drug discovery.

>>dekhn+4x
I'm really curious about this space: what types of simulation/prediction (if any) do you see as being the most useful?

Edit to clarify my question: What useful techniques 1. Exist and are used now, and 2. Theoretically exist but have insurmountable engineering issues?