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Chemistry Nobel: Computational protein design and protein structure prediction

nobelprize.org

101–110 of 343 posts

Re: Chemistry Nobel: Computational protein design and protein structure prediction

#101
I think putting AlphaFold here was premature; it might not age well. AlphaFold is an impressive achievement but it simply has not "cracked the code for protein folding" - about 1/3rd of its predictions are too uncertain to be usable, it says nothing about dynamics, suffers from the same ML problems of failing on uncommon structures, and I was surprised to learn that many of its predictions are incorrect because it ignores topological constraints[1]. To be clear, these are constructive criticisms of AlphaFold in isolation, my grumpiness is directed at the Nobel committee. "Cracked the code for protein folding" is simply not true; it is an ML approach with high accuracy that suffers the same ML limitations of failing to generalize or failing to understand deeper principles like R^3 topology that cannot be gleaned stochastically.

More significantly: it has yet to be especially impactful in biochemistry research, nor has its results really been carefully audited. Maybe it will turn out to deserve the prize. But the committee needed to wait. I am concerned that they got spun by Google's PR campaign - or, considering yesterday's prize, Big Tech PR in general.

[1] https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10672856/

Re: Chemistry Nobel: Computational protein design and protein structure prediction

#102
post #5
post #2

People joked maybe the Nobel committee is holding some AI stocks. Now I start to wonder if that is true...

Maybe the transformers authors will win Literature.

I would actually not even be mad. After all it is fundamental change in production of literature works.

Re: Chemistry Nobel: Computational protein design and protein structure prediction

#103

While I am skeptical about yesterdays award in physics, these are totally deserved and spot on. There are few approaches that will accelerate the field of drug development and chemistry as a whole in a way that the works of these three people will. Congratulations!

I was just wondering when they were going to award the alphafold2 guys the nobel after after seeing Hinton win the physics one. 100% agree, all three of them totally deserve this one. Baker's lab is pretty much keeping Deepmind in check at this point and ensuring open source research is keeping up. Hats off

Baker has been in the protein folding game for a long time and was the leader before Alphafold came in... His generative paper came out what last year (2023)?

I mean this is a fast award cycle.

Re: Chemistry Nobel: Computational protein design and protein structure prediction

#104

Earlier quoted context omitted.

He's founder and CEO of the AI lab that build Alphafold?

Then maybe Sergey and Larry should also get the prize since they founded Google, which owns Deepmind?

They bought it and it runs autonomously (or did mostly)

Re: Chemistry Nobel: Computational protein design and protein structure prediction

#105
post #19

The AlphaFold paper has countless authors, many researchers and company resources underlying it. Hassabis’ contribution is management of resources and entrepreneurship, not the actual science. There are hundreds of thousands of scientists out there doing deep technical work, and they aren’t recognized. I think we might be the end of it, as the emphasis shifts to commercialization and product development. These AI dem…

So can we expect that Sam Altman will be honored with Nobel prize 2025? After all physics prize went to AI researchers this year, and chemistry prize went to an organizational head.

You're really conflating things. Altman is no Hassabis.

Just because there is a ton of hype from OpenAI doesn't detract from what DeepMind has done. AlphaGo anybody?

Are we really already forgetting what a monumental problem protein folding was, decades of research, and AlphaFold came in and revolutionized it overnight.

We are pretty jaded these days when miracles are happening all the time and people are like "yeah, but he's just a manager 'now', what have they done for me in the last few days".

Re: Chemistry Nobel: Computational protein design and protein structure prediction

#106
post #68

While I am skeptical about yesterdays award in physics, these are totally deserved and spot on. There are few approaches that will accelerate the field of drug development and chemistry as a whole in a way that the works of these three people will. Congratulations!

The physics prize should have went to Elon Musk! Also I really hope the Nobel Prize of Economics goes to Bill Gates! He facilitated sooo much advances by releasing Excel that this must be recognized! And based on this year's announcements so far I am not sure that my sarcastic comments should be taken as a joke!

Except Excel has introduced way to many bugs and how many people has it killed?

Re: Chemistry Nobel: Computational protein design and protein structure prediction

#107

I think putting AlphaFold here was premature; it might not age well. AlphaFold is an impressive achievement but it simply has not "cracked the code for protein folding" - about 1/3rd of its predictions are too uncertain to be usable, it says nothing about dynamics, suffers from the same ML problems of failing on uncommon structures, and I was surprised to learn that many of its predictions are incorrect because it ig…

I think looking back five years from now, this will be viewed as another Kissinger/Obama but wrt STEM. Given far too prematurely under pressure to keep up with the Joneses/chase the hype.

Re: Chemistry Nobel: Computational protein design and protein structure prediction

#108
post #41
post #24

Here's a direct quote from the Alphafold paper: "These authors contributed equally: John Jumper, Richard Evans, Alexander Pritzel, Tim Green, Michael Figurnov, Olaf Ronneberger, Kathryn Tunyasuvunakool, Russ Bates, Augustin Žídek, Anna Potapenko, Alex Bridgland, Clemens Meyer, Simon A. A. Kohl, Andrew J. Ballard, Andrew Cowie, Bernardino Romera-Paredes, Stanislav Nikolov, Rishub Jain, Demis Hassabis"

Here's 8 densely printed pages of contributors to a discovery that lead to a Nobel prize: https://arxiv.org/pdf/1207.7214#page=26 Guess how many of them were included in the prize. It's a shame that the Nobel committee shies away from awarding it to institutions, but the AlphaFold prize doesn't even make the top 10 in a list of most controversial omissions from a Nobel prize. It's a simple case of lab director gets t…

It's not a case of shying away from it: the rules of the prize don't allow it.

Re: Chemistry Nobel: Computational protein design and protein structure prediction

#109
post #35
post #24

Here's a direct quote from the Alphafold paper: "These authors contributed equally: John Jumper, Richard Evans, Alexander Pritzel, Tim Green, Michael Figurnov, Olaf Ronneberger, Kathryn Tunyasuvunakool, Russ Bates, Augustin Žídek, Anna Potapenko, Alex Bridgland, Clemens Meyer, Simon A. A. Kohl, Andrew J. Ballard, Andrew Cowie, Bernardino Romera-Paredes, Stanislav Nikolov, Rishub Jain, Demis Hassabis"

They didnt give the award to the paper

At least they could have read it before awarding the price.
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