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Comment by colingauvin | Hacker News Reader

>DeepMind started developing AlphaFold in 2018. In 2020, it was recognized as a solution to humanity's 50-year-old "protein folding problem," which sought to answer how amino acids automatically fold into complex 3D shapes.

This is not even close to reality. AlphaFold is not a solution to the protein folding problem, it's (useful) pattern matching to the end state of solved folded protein (in situations that can be pattern matched). If this is considered "solving the protein folding problem" then X-ray crystallography solved it first, 75 years ago.

There is essentially zero "how" information coming to us from AlphaFold. This type of reporting is incorrect, and irresponsible to the folks that are still working on that how problem.

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Pissed me off since day one that got by with that "solving" shit. Not to downplay what they did, but it had little to do with the problem as it's been understood to mean.

And to be clear I do think it was nobel worthy.

I do not think it was Nobel worthy for Hassam et. al.

David Baker is the GOAT of that field, it should have been awarded to him only.

I know baker's work quite well, no it shouldn't have

Can you name others that deserved it more?

For what? I thought your trying to argue only baker deserved solo compared to what happened?

If you're asking about solving the actual folding problem? Probably Dill, Onuchic, Wolynes, maybe Sosnick would be top of my list off the top of my head. Anfinsen if he was alive.

Yes, they have a probabilistic model, not an analytical solution.

OTOH I don't think they made up the "solved" label - the CASP benchmark had always considered reaching the AlphaFold level of predictive accuracy (within error tolerance of our ability to experimentally verify via X-ray crystallography etc) as "solving" the problem.

CASP is explicitly structure prediction. That's not the folding problem.

Yes, but in the AlphaFold documentary they did explicitly mention "solving" CASP as the target.

The kind of solution you want may not be possible.

There is no guarantee that a tractable method exists to analytically invert protein folding. Data-driven methods like alphafold may be the only option.

That has nothing to do with the fact that the article is inaccurate.

Tell that to the nobel prize committee.

The article is fine. AlphaFold is widely regarded as "solving" protein folding.

Gemini says it did not solve the physics of how a protein actually folds.

This has nothing to do with what I am talking about.

It's an NP hard problem.

To SOLVE it would easily win the Nobel, possibly the Turing and more.

Designer proteins would change the world and medicine also in unimaginable ways.

Yes and correct me if I'm wrong, but they never did deeper work on dynamics. I think that's very telling.

they're probably referring to CASP13/14

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