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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

#21

Post by dekhn »

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…

I am not aware of anybody currently criticiszing AF2's abilities outside of its training set. In fact the most recent papers (written by crystallographers) they are mostly arguing about atomic-level details of side chains at this point.

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

#22

Post by throwtappedmac »

s1artibartfast wrote: post #2

The article was heavy on the free research aspect, but light on the commercial application. I'm curious about the business strategy. Does Google intend to license out tools, partner, or consult for commercial partners?

[flagged]

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

#23

Post by dekhn »

joshuamcginnis wrote: post #17
tea-coffee wrote: post #11

This is a basic question, but how is the accuracy of the predicted biomolecular interactions measured? Are the predicted interactions compared to known interactions? How would the accuracy of predicting unknown interactions be assessed?

Accuracy can be assessed two main ways: computationally and experimentally. Computationally, they would compare the predicted structures and interactions with known data from databases like PDB (Protein Database). Experimentally, they can use tools like x-ray crystallography and NMR (nuclear magnetic resonance) to obtain the actual molecule structure and compare it to the predicted result. The outcomes of each approa…

AlphaFold very explicitly (unless something has changed) removes NMR structures as references because they are not accurate enough. I have a PhD in NMR biomolecular structure and I wouldn't trust. the structures for anything.

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

#24

Post by mhrmsn »

Metacelsus wrote: post #4

From: https://www.nature.com/articles/d41586-024-01383-z >Unlike RoseTTAFold and AlphaFold2, scientists will not be able to run their own version of AlphaFold3, nor will the code underlying AlphaFold3 or other information obtained after training the model be made public. Instead, researchers will have access to an ‘AlphaFold3 server’, on which they can input their protein sequence of choice, alongside a selection of…

Also no commercial use, from the paper:

> AlphaFold 3 will be available as a non-commercial usage only server at https://www.alphafoldserver.com, with restrictions on allowed ligands and covalent modifications. Pseudocode describing the algorithms is available in the Supplementary Information. Code is not provided.

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

#25

Post by dekhn »

weregiraffe wrote: post #3

s/predicts/attempts to predict

AlphaFold has been widely validated- it's now appreciated that its predictions are pretty damn good, with a few important exceptions, instances of which are addressed with the newer implementation.

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

#26

Post by ranger_danger »

Metacelsus wrote: post #4

From: https://www.nature.com/articles/d41586-024-01383-z >Unlike RoseTTAFold and AlphaFold2, scientists will not be able to run their own version of AlphaFold3, nor will the code underlying AlphaFold3 or other information obtained after training the model be made public. Instead, researchers will have access to an ‘AlphaFold3 server’, on which they can input their protein sequence of choice, alongside a selection of…

Not just unfortunate, but doesn't this make it completely untrustable? How can you be sure the data was not modified in any way? How can you verify any results?

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

#27

Post by [deleted] »

Metacelsus wrote: post #4

From: https://www.nature.com/articles/d41586-024-01383-z >Unlike RoseTTAFold and AlphaFold2, scientists will not be able to run their own version of AlphaFold3, nor will the code underlying AlphaFold3 or other information obtained after training the model be made public. Instead, researchers will have access to an ‘AlphaFold3 server’, on which they can input their protein sequence of choice, alongside a selection of…

[deleted]

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

#29

Post by COGlory »

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.

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

#30

Post by ebiester »

rolph wrote: post #19
Metacelsus wrote: post #4

From: https://www.nature.com/articles/d41586-024-01383-z >Unlike RoseTTAFold and AlphaFold2, scientists will not be able to run their own version of AlphaFold3, nor will the code underlying AlphaFold3 or other information obtained after training the model be made public. Instead, researchers will have access to an ‘AlphaFold3 server’, on which they can input their protein sequence of choice, alongside a selection of…

in other words, this has been converted to a novelty, and has no use for scientific purposes.

No. It just means that scientific purposes will have an additional tax paid to google. This will likely reduce use in academia but won't deter pharmaceutical companies.
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