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AlphaFold 3 predicts the structure and interactions of life's molecules

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Re: AlphaFold 3 predicts the structure and interactions of life's molecules

#421

Post by flobosg »

COGlory wrote: post #29
renonce wrote: post #5

> What is different about the new AlphaFold3 model compared to AlphaFold2? > AlphaFold3 can predict many biomolecules in addition to proteins. AlphaFold2 predicts structures of proteins and protein-protein complexes. AlphaFold3 can generate predictions containing proteins, DNA, RNA, ions,ligands, and chemical modifications. The new model also improves the protein complex modelling accuracy. Please refer to our paper…

>So the criticism towards AlphaFold 2 will likely still apply? For example, it’s more accurate for predicting structures similar to existing ones, and fails at novel patterns? Yes, and there is simply no way to bridge that gap with this technique. We can make it better and better at pattern matching, but it is not going to predict novel folds.

> but it is not going to predict novel folds

https://www.nature.com/articles/s42003-022-03357-1

Re: AlphaFold 3 predicts the structure and interactions of life's molecules

#422

Post by flobosg »

staticautomatic wrote: post #380
rolph wrote: post #39

Earlier quoted context omitted.

problem is biomolecules, are "chaperoned" to fold properly, only specific regions such as, alpha helix, or beta pleatedsheet will fold de novo. Chaperone (protein) https://en.wikipedia.org/wiki/Chaperone_(protein)

In principle couldn’t we just incorporate knowledge about chaperones into the model?

In a way it is already incorporated. Broadly speaking, chaperones function by restricting the available conformational sampling space for the protein to fold. Some researchers even consider the ribosome as a chaperone of sorts for the nascent protein chain it synthetizes.

Protein structure prediction methods do the same: they find ways of restricting the conformational space to explore, in hopes of finding the global minimum-energy conformation representing the native structure of the protein.

Re: AlphaFold 3 predicts the structure and interactions of life's molecules

#423

Post by Syzygies »

gajnadsgjoas wrote: post #409

Can someone tell me what are the direct implication of this? I often see "helps with a drug design" but I'm too far from this industry and have never seen an example of such drugs

We're this much closer to being hacked?

Re: AlphaFold 3 predicts the structure and interactions of life's molecules

#424

Post by [deleted] »

roody15 wrote: post #219

I wonder in the not too distant future if these AI predictions could be explained back into “humanized” understanding. Much like ChatGPT can simplify complex topics … cold the model in the future provide feedback to researchers why it is making this prediction?

[deleted]

Re: AlphaFold 3 predicts the structure and interactions of life's molecules

#425

Post by mda »

porphyra wrote: post #381
nybsjytm wrote: post #62

Important caveat: it's only about 70% accurate. Why doesn't the press release say this explicitly? It seems intentionally misleading to only report accuracy relative to existing methods, which apparently are just not so good (30%, 50% in various settings). https://www.fastcompany.com/91120456/deepmind-alphafold-3-dn...

They also had a headline for Alphazero that convinced everyone that they crushed Stockfish and that classical chess engines were stuff of the past, when in fact it was about 50 elo better than the Stockfish version they were testing against, or roughly the same as how much Stockfish improves each year.

Alphazero indeed crushed stockfish with a novel technique, I think it deserved all the praise.

Re: AlphaFold 3 predicts the structure and interactions of life's molecules

#426

Post by jprete »

toxik wrote: post #257
jprete wrote: post #194

Earlier quoted context omitted.

The goal of science has always been to discover underlying principles and not merely to predict the outcome of experiments. I don't see any way to classify an opaque ML model as a scientific artifact since by definition it can't reveal the underlying principles. Maybe one could claim the ML model itself is the scientist and everyone else is just feeding it data. I doubt human scientists would be comfortable with that…

Kepler famously compiled troves of data on the night sky, and just fitted some functions to them. He could not explain why but he could say what. Was he not a scientist?

He did attempt to explain why. Wikipedia: "On 4 February 1600, Kepler met Tycho Brahe....Tycho guarded his data closely, but was impressed by Kepler's theoretical ideas and soon allowed him more access. Kepler planned to test his theory from Mysterium Cosmographicum based on the Mars data, but he estimated that the work would take up to two years (since he was not allowed to simply copy the data for his own use)."

Re: AlphaFold 3 predicts the structure and interactions of life's molecules

#427

Post by baq »

BriggyDwiggs42 wrote: post #411
hackernewds wrote: post #405

Earlier quoted context omitted.

These are very specific ideas you have..

It’s very frustrating when people consider the possession of information equivalent to malice. It suggests that the right way to run society is to keep people stupid and harmless.

Harmless is enough. The smart ones will figure out that knowing shortens lives.

Re: AlphaFold 3 predicts the structure and interactions of life's molecules

#429

Post by borgdefense »

Balgair wrote: post #235
amitport wrote: post #216

Earlier quoted context omitted.

Consider that humans also learn from other humans, and sometimes surpass their teachers. A bit more comfortable?

Ahh, but the new young master is able to explain their work and processes to the satisfaction of the old masters. In the 'Science' of our modern times it's a requirement to show your work (yes, yes, I know about the replication crisis and all that terrible jazz). Not being able to ascertain how and why the ML/AI is achieving results is not quite the same and more akin to the alchemists and sorcerers with their cypher…

[flagged]

Re: AlphaFold 3 predicts the structure and interactions of life's molecules

#430

Post by nybsjytm »

moomin wrote: post #410
dekhn wrote: post #213

Earlier quoted context omitted.

The way I think about this (specifically, deepmind not publishing their code or sharing their exact experimental results): advanced science is a game played by the most sophisticated actors in the world. Demis is one of those actors, and he plays the games those actors play better than anybody else I've ever seen. Those actors don't care much about the details of any specific system's accuracy: they care to know that…

Anyone remember how he marketed his computer games?

No, how?
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