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?
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
#12From: 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…
The second amendment prevents the government's overreaching perversion to restrict me from having the ability to print biological weapons from the comfort of my couch.
Google has no such restriction.
Re: AlphaFold 3 predicts the structure and interactions of life's molecules
#13This reminds me of Google’s claim that another “AI” discovered millions of new materials. The results turned out to be a lot of useless noise but that was only apparent after actual expert spent hundreds of hours reviewed the results[0]
0: https://www.404media.co/google-says-it-discovered-millions-o...
Re: AlphaFold 3 predicts the structure and interactions of life's molecules
#14Re: AlphaFold 3 predicts the structure and interactions of life's molecules
#15> 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…
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Re: AlphaFold 3 predicts the structure and interactions of life's molecules
#16From: 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…
That sucks a bit. I was just wondering why they are touting that 3rd party company in their own blog post, who commercialise research tools, as well. Maybe there are some corporate agreements with them that prevents them from opening the system... Imagine the goodwill for humanity for releasing these pure research systems for free. I just have a hard time understanding how you can motivate to keep it closed. Let's ho…
Isomorphic Labs? That's an Alphabet owned startup run by Denis Hassabis that they created to commercialise the Alphafold work, so it's not really a 3rd party at all.
Re: AlphaFold 3 predicts the structure and interactions of life's molecules
#17This 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 approach would be fed back into the model for refining future predictions.
Re: AlphaFold 3 predicts the structure and interactions of life's molecules
#18This reminds me of Google’s claim that another “AI” discovered millions of new materials. The results turned out to be a lot of useless noise but that was only apparent after actual expert spent hundreds of hours reviewed the results[0] 0: https://www.404media.co/google-says-it-discovered-millions-o...
The alphafold work has been used across the industry (successfully, in the sense of blind prediction), and has been replicated independently. The work on alphafold will likely net Demis and John a Nobel prize in the next few years.
(that said, one should always inspect Google publications with a fine-toothed comb and lots of skepticism, as they have a tendency to juice the results)
Re: AlphaFold 3 predicts the structure and interactions of life's molecules
#19From: 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.
Re: AlphaFold 3 predicts the structure and interactions of life's molecules
#20s/predicts/attempts to predict
A prediction is a prediction; it's not necessarily a correct prediction.
The weatherman predicts the weather, even if he's sometimes wrong, we don't say "he attempts to predict" the weather.