4 ms·

> FTA: For one thing, only two-thirds of DeepMind’s solutions were comparable to the experimentally determined structure of the protein. This seems to be the c

by titzer 6y ago

> FTA: For one thing, only two-thirds of DeepMind’s solutions were comparable to the experimentally determined structure of the protein. This seems to be the core of the article's arguments. Is this ratio high enough to claim the problem is "solved"?

throwaway2245 6y ago
If your goal is drug discovery by checking out relevant protein structures, then you'll be lucky with useful structure information ~2/3 of the time (perhaps less, if you are depending on interactions of more than one protein). If it was possible to accelerate drug discovery by looking at computed protein structures rather than protein structures established experimentally, it has now become plausible to do so. It has crossed a tipping point. Since I'm not aware that there has been any drug discovery that has strongly depended on computational protein folding, this possible benefit remains to be seen. [I worked in a lab which was heavily involved in CASP, the protein folding competition, but I was not myself involved]
mantap 6y ago
Algorithms only get better. Did Google "solve" computer Go when AlphaGo beat Lee Sedol, when Master beat Ke Jie, or when AlphaZero learned Go from scratch? Even though Google only won 4/5 games against Lee Sedol, that was the moment that sticks in peoples minds as when Google solved the problem of computer Go. What happened afterwards was a process of perfecting the algorithm. It seems likely the next few years will bring the same for AlphaFold.
- titzer 6y ago
  But in this case AlphaFold is only marginally better than other algorithms. Since we are comparing computer algorithms (and not a human to an algorithm), it'd be like saying Usain Bolt "solved" the 100m dash when he set a new world record. Is it solved though, without knowing how fast those other algorithms are advancing?
  - visarga 6y ago
    have you seen the performance graph? it went from 40% (other teams) to 60% (DeepMind 2 years ago) to 92% now.
  - yread 6y ago
    here is a nice case where alphafold did way better than others https://twitter.com/TassosPerrakis/status/1333535594002132996/photo/1 https://twitter.com/TassosPerrakis/status/133353559400213299... Tassos is also a professor in structural biology. Discovering structures the experimental way. EDIT: on the other hand he also agrees that it's not the end of experimental structural biology https://twitter.com/TassosPerrakis/status/1334024678311079936 https://twitter.com/TassosPerrakis/status/133402467831107993...
  - tigershark 6y ago
    No it’s not. AlphaFold is a huge advancement on all the other solutions. Solutions that were based on the already massive improvement that DeepMind brought in the previous edition.

by titzer 6y ago

throwaway2245 6y ago

If your goal is drug discovery by checking out relevant protein structures, then you'll be lucky with useful structure information ~2/3 of the time (perhaps less, if you are depending on interactions of more than one protein). If it was possible to accelerate drug discovery by looking at computed protein structures rather than protein structures established experimentally, it has now become plausible to do so. It has crossed a tipping point. Since I'm not aware that there has been any drug discovery that has strongly depended on computational protein folding, this possible benefit remains to be seen. [I worked in a lab which was heavily involved in CASP, the protein folding competition, but I was not myself involved]

mantap 6y ago

Algorithms only get better. Did Google "solve" computer Go when AlphaGo beat Lee Sedol, when Master beat Ke Jie, or when AlphaZero learned Go from scratch? Even though Google only won 4/5 games against Lee Sedol, that was the moment that sticks in peoples minds as when Google solved the problem of computer Go. What happened afterwards was a process of perfecting the algorithm. It seems likely the next few years will bring the same for AlphaFold.

titzer 6y ago
But in this case AlphaFold is only marginally better than other algorithms. Since we are comparing computer algorithms (and not a human to an algorithm), it'd be like saying Usain Bolt "solved" the 100m dash when he set a new world record. Is it solved though, without knowing how fast those other algorithms are advancing?
- visarga 6y ago
  have you seen the performance graph? it went from 40% (other teams) to 60% (DeepMind 2 years ago) to 92% now.
- yread 6y ago
  here is a nice case where alphafold did way better than others https://twitter.com/TassosPerrakis/status/1333535594002132996/photo/1 https://twitter.com/TassosPerrakis/status/133353559400213299... Tassos is also a professor in structural biology. Discovering structures the experimental way. EDIT: on the other hand he also agrees that it's not the end of experimental structural biology https://twitter.com/TassosPerrakis/status/1334024678311079936 https://twitter.com/TassosPerrakis/status/133402467831107993...
- tigershark 6y ago
  No it’s not. AlphaFold is a huge advancement on all the other solutions. Solutions that were based on the already massive improvement that DeepMind brought in the previous edition.