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Chemistry Nobel: Computational protein design and protein structure prediction

nobelprize.org

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

#191

Post by throwawaymaths »

dekhn wrote: post #153

I wasn't expecting to see David Baker in the list (just Demis and John). But I'm really glad to see it... David is a great guy. At CASP (the biannual protein structure prediction competition) around 2000, I sat down with David and told him that eventually machine learning would supplant humans at structure prediction (at the time Rosetta was already the leading structure prediction/design tool, but was filled with a…

Refreshingly good. Bakers "early" (not really early, but earlier than AlphaFold) work (having humans with no background solve folds) really laid the groundwork to proving that heuristic methods were likely to outperform physical forcefield and ab initio/DFT methods for structure prediction. And AI structure prediction if nothing else is heuristic protein folding.

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

#192

Post by timmg »

nextworddev wrote: post #135
singularity2001 wrote: post #128

Earlier quoted context omitted.

whose father was one of the leading local industrialists (installing the first electric lighting for the 1885 Munich Oktoberfest)

It’s fascinating how the affluent backgrounds of many famous scientists and entrepreneurs are downplayed. Eg Warren Buffet, Jeff Bezos, etc

There’s another side to this: if you accept the idea of “nature” — genes capable of carrying “talent” (in some sense) — it should be common for children of talented people to be talented.

Of course, talent doesn’t always mean prosperity. But in a society modeled on meritocracy, it often will.

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

#193

Post by InkCanon »

aithrowawaycomm wrote: post #146
InkCanon wrote: post #107

Earlier quoted context omitted.

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.

I am not so confident or dismissive: the real problem is that testing millions of predictions (or any fairly bold scientific development like AlphaFols) takes time, and that time simply has not elapsed. Some of the criticisms I identified might be low-hanging fruit that in 5 years will be seen as minor corrections - but we're still discovering the things that need to be corrected. It is concerning that the prize anno…

I have the same views as you (although admittedly the Kissinger comparison didn't convey that, because we all know how that turned out). It's at best quite premature. At worst, should never have been given in hindsight. Will probably land somewhere in between.

Second point is spot on. I really, really hope they didn't just fall for what is frankly a bit of SV style press release meant to hype things. Similar work was done on crystal structures with some massive number reported. It's a vastly other thing than the implied meaning that they are now fully understood and able to be used in some way.

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

#194

Post by londons_explore »

cmavvv wrote: post #136
mhrmsn wrote: post #84

Great achievement, although I think it's interesting that this Nobel prize was awarded so early, with "the greatest benefit on mankind" still outstanding. Are there already any clinically approved drugs based on AI out there I might have missed? In comparison, the one for lithium batteries was awarded in 2019, over 30 years after the original research, when probably more than half of the world's population already us…

Given that drugs take around 10 years to get to market, and that some time is needed for industrial adoption as well, it's not very reasonable to expect clinically approved drugs before a few years.

> around 10 years to get to market

This is really sad. A new recipe for feeding honeybees to make tastier honey could get to market in perhaps a month or two. All the chemical reactions happening in the bees gut and all the chemicals in the resulting honey are unknown, yet within a matter of weeks its being eaten.

Yet if we find a new way of combining chemicals to cure cancer, it takes a decade before most can benefit.

I feel like we don't balance our risks vs rewards well.

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

#195

Post by dekhn »

fedeb95 wrote: post #166
eig wrote: post #117

I think I disagree with most of the comments here stating it’s premature to give the Nobel to AlphaFold. I’m in biotech academia and it has changed things already. Yes the protein folding problem isn’t “solved” but no problem in biology ever is. Comparing to previous bio/chem Nobel winners like Crispr, touch receptors, quantum dots, click chemistry, I do think AlphaFold already has reached sufficient level of impact.

what has changed? I think people need more from a comment than blind trust.

It solidly answered the question: "Is evolutionary sequence relationship and structure data sufficient to predict a large fraction of the structures that proteins adopt". the answer, surprising few, is that the data we have indeed can be used to make general predictions (even outside of the training classes), and also surprising many, that we can do so with a minimum of evolutionary sequence data.

That people are arguing about the finer details of what it gets wrong is support for its value, not a detriment.

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

#196

Post by flobosg »

boxed wrote: post #89

I think it's still too early to know if AlphaFold is a massively overfitted statistical model that will utterly fail on novel structures.

AlphaFold2 has correctly predicted novel folds: https://www.nature.com/articles/s42003-022-03357-1

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

#197

Post by afthonos »

hyperbrainer wrote: post #185
afthonos wrote: post #150

Earlier quoted context omitted.

Can they? I mean, in the sense that you can yolo anything, sure, but the prizes were designed in a time when it was (more) reasonable to award them to individuals, and they are defined in a will. There may not be a mechanism for updating the standards.

Yes, they can. In 1901, science was not nearly as collaborative as it is today. Especially considering the need for a Nobel Prize to be experimental and the fact that most major labs today _need_ dozens of people.

That…has nothing to do with my question. It was a procedural and legal question, not an abstract moral one.

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

#198

Post by achierius »

hyperbrainer wrote: post #185
afthonos wrote: post #150

Earlier quoted context omitted.

Can they? I mean, in the sense that you can yolo anything, sure, but the prizes were designed in a time when it was (more) reasonable to award them to individuals, and they are defined in a will. There may not be a mechanism for updating the standards.

Yes, they can. In 1901, science was not nearly as collaborative as it is today. Especially considering the need for a Nobel Prize to be experimental and the fact that most major labs today _need_ dozens of people.

He asked _can_ not _should_: what is the legal mechanism for doing so? Personally I don't doubt there is one but I don't think you know it off the top of your head, so I don't see it as fair to disparage OP for not knowing either.

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

#199

Post by stanford_labrat »

exmadscientist wrote: post #53
gilleain wrote: post #8

David Baker (and colleagues) have always done good work. I guess google have done some things also. (lol - one of the PDF attachments to that page is 'Illustration: A string of amino acids' : actually it's a bit better than the title implies :). Actually, Figure 2 - "How does AlfaFold2 Work?" is impressive to fit that on one page. Nice.

It is well known around here that Baker does very, very little of the work. He is extremely good at putting his name on his students' work though (this is par for the course in academia)... and removing theirs (this is the bad part). At least he bribes them with lots of happy hours!

username...checks out

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

#200

Post by [deleted] »

DevX101 wrote: 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"

[deleted]
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