4 ms·

You are misunderstanding me. There is theory about how atoms etc. interact. We cannot use that to predict shape (at present) but at the same time there is no fo

You are misunderstanding me. There is theory about how atoms etc. interact. We cannot use that to predict shape (at present) but at the same time there is no force etc. missing as far as our current understanding is concerned (at most basic level no physics seem to missing). So predictions seem at least possible or rather are not blocked. On the other hand, trying to use an AI to make predictions which atom of a radioactive element was to decay next would run afoul of current theories.

PaulDavisThe1st 5y ago
People have worked on "theory-based" protein structure prediction for 35-40 years. It essentially went nowhere. It is theoretically possible? Probably. Does it have anything to do with how AlphaFold works? no. Does it have anything to do with verifying AlphaFold's predictions? no.
- RandomLensman 5y ago
  I never claimed it has anything to do with verifying the predictions. I am saying it allows such predictions.
  - PaulDavisThe1st 5y ago
    But it doesn't! It isn't theory that led us to notice that (almost all) proteins fold naturally into the same shape every time they are denatured and annealed. It was simple experimentation. The attempts to create a theory of how that happens have been measured by the success of those attempted theories to make successful structure predictions. They have failed (pretty dismally in most cases). So there is no theory that allows us to make such predictions. We simply have experimental evidence that proteins can adopt their "normal" structure by themselves, essentially every time. We have no functioning theory of how they do this, and no way to use this non-existent theory to make predictions.
    - RandomLensman 5y ago
      You are still misunderstanding me. I am not saying we have a theory of how proteins fold. We have theories on force interactions between atoms. Those theories are pretty complete and do not say that predictions of protein shapes are impossible. We are not blocked from trying, like, for example, in predicting decaying atoms. So trying stuff like AlphaFold is not going against current understanding. My point is much more basic, if you will. So I meant "allow" as in there is no theory saying that we cannot do it. Not that we have a theory how to do it.

PaulDavisThe1st 5y ago

People have worked on "theory-based" protein structure prediction for 35-40 years. It essentially went nowhere. It is theoretically possible? Probably. Does it have anything to do with how AlphaFold works? no. Does it have anything to do with verifying AlphaFold's predictions? no.

RandomLensman 5y ago
I never claimed it has anything to do with verifying the predictions. I am saying it allows such predictions.
- PaulDavisThe1st 5y ago
  But it doesn't! It isn't theory that led us to notice that (almost all) proteins fold naturally into the same shape every time they are denatured and annealed. It was simple experimentation. The attempts to create a theory of how that happens have been measured by the success of those attempted theories to make successful structure predictions. They have failed (pretty dismally in most cases). So there is no theory that allows us to make such predictions. We simply have experimental evidence that proteins can adopt their "normal" structure by themselves, essentially every time. We have no functioning theory of how they do this, and no way to use this non-existent theory to make predictions.
  - RandomLensman 5y ago
    You are still misunderstanding me. I am not saying we have a theory of how proteins fold. We have theories on force interactions between atoms. Those theories are pretty complete and do not say that predictions of protein shapes are impossible. We are not blocked from trying, like, for example, in predicting decaying atoms. So trying stuff like AlphaFold is not going against current understanding. My point is much more basic, if you will. So I meant "allow" as in there is no theory saying that we cannot do it. Not that we have a theory how to do it.