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> Has protein folding been solved? Yes. No. Look a the actual competition results. > As a practitioner, what I want to be able to do is pull a sequence that I

by twic 6y ago

> Has protein folding been solved? Yes. No. Look a the actual competition results. > As a practitioner, what I want to be able to do is pull a sequence that I've retrieved from DNA, drop it into a computer, and get the structure out. Intuitive insight can FOLLOW from those results. According to the competition results, you cannot do that using AlphaFold2.

deeviant 6y ago
"We have been stuck on this one problem – how do proteins fold up – for nearly 50 years. To see DeepMind produce a solution for this, having worked personally on this problem for so long and after so many stops and starts, wondering if we’d ever get there, is a very special moment. " - Professor John Moult Co-Founder and Chair of CASP, University of Maryland Gee, the Co-Founder of the competition calls it a solution. I wonder if that might be because this is a solution to the problem as he A) Knows much more about the problem than you B) has actually personally seen the results and C) has far more context than you to base his decision to call it a solution.
- twic 6y ago
  He should also look a the actual competition results.
nl 6y ago
According to the competition organisers, you can: So Lupas set a special challenge: a membrane protein from a species of archaea, an ancient group of microbes. For 10 years, his research team tried every trick in the book to get an x-ray crystal structure of the protein. “We couldn’t solve it.” But AlphaFold had no trouble. It returned a detailed image of a three-part protein with two long helical arms in the middle. The model enabled Lupas and his colleagues to make sense of their x-ray data; within half an hour, they had fit their experimental results to AlphaFold’s predicted structure. “It’s almost perfect,” Lupas says. “They could not possibly have cheated on this. I don’t know how they do it.” Sure, you want to validate thing experimentally, but that isn't different to imaging. [1] https://www.sciencemag.org/news/2020/11/game-has-changed-ai-triumphs-solving-protein-structures https://www.sciencemag.org/news/2020/11/game-has-changed-ai-...
- dnautics 6y ago
  just for clarification, I don't know for certain, but it sounds like this is what they are talking about in science-journalism speak: https://news.ycombinator.com/reply?id=25262458&goto=threads%3Fnext%3D25283955%26id%3Ddnautics%2325262458 https://news.ycombinator.com/reply?id=25262458&goto=threads%... So they bootstrapped the phases of the X-ray diffraction pattern with the phases from AlphaFold. This does mean, though, that we must be critical - it is possible that they are converging to nonsense that AlphaFold has generated. To be truly sure, you must have some sort of independent confirmation. Might still be "good enough" depending on what your application is.

by twic 6y ago

deeviant 6y ago

"We have been stuck on this one problem – how do proteins fold up – for nearly 50 years. To see DeepMind produce a solution for this, having worked personally on this problem for so long and after so many stops and starts, wondering if we’d ever get there, is a very special moment. " - Professor John Moult Co-Founder and Chair of CASP, University of Maryland Gee, the Co-Founder of the competition calls it a solution. I wonder if that might be because this is a solution to the problem as he A) Knows much more about the problem than you B) has actually personally seen the results and C) has far more context than you to base his decision to call it a solution.

twic 6y ago
He should also look a the actual competition results.

nl 6y ago

According to the competition organisers, you can: So Lupas set a special challenge: a membrane protein from a species of archaea, an ancient group of microbes. For 10 years, his research team tried every trick in the book to get an x-ray crystal structure of the protein. “We couldn’t solve it.” But AlphaFold had no trouble. It returned a detailed image of a three-part protein with two long helical arms in the middle. The model enabled Lupas and his colleagues to make sense of their x-ray data; within half an hour, they had fit their experimental results to AlphaFold’s predicted structure. “It’s almost perfect,” Lupas says. “They could not possibly have cheated on this. I don’t know how they do it.” Sure, you want to validate thing experimentally, but that isn't different to imaging. [1] https://www.sciencemag.org/news/2020/11/game-has-changed-ai-triumphs-solving-protein-structures https://www.sciencemag.org/news/2020/11/game-has-changed-ai-...

dnautics 6y ago
just for clarification, I don't know for certain, but it sounds like this is what they are talking about in science-journalism speak: https://news.ycombinator.com/reply?id=25262458&goto=threads%3Fnext%3D25283955%26id%3Ddnautics%2325262458 https://news.ycombinator.com/reply?id=25262458&goto=threads%... So they bootstrapped the phases of the X-ray diffraction pattern with the phases from AlphaFold. This does mean, though, that we must be critical - it is possible that they are converging to nonsense that AlphaFold has generated. To be truly sure, you must have some sort of independent confirmation. Might still be "good enough" depending on what your application is.