5 ms·
> We are effectively no closer to understanding how proteins fold, nor are we closer to being able to predict how a protein folds without any a priori informati
by ruuda 4y ago
> We are effectively no closer to understanding how proteins fold, nor are we closer to being able to predict how a protein folds without any a priori information.
Isn't that a bit like saying about image classifiers, that we still don't _understand_ how to recognize cat pictures, and that we couldn't do it without a large set of training data?
(To an extent this is true, that's also why a lot of work goes into interpretability and attribution in models.)
- flobosg 4y agoAlphaFold knows very little about the physicochemical mechanisms governing protein folding and doesn’t give any new insights either. The way it samples conformational space is very different from Folding@home’s molecular dynamics based approach, for instance. To describe the folding of a protein chain, a “picture” of its lowest energy conformation (which is the goal of AlphaFold—and any structural modelling tool) is not enough. We rather need a “movie” showing the steps said chain undergoes, from an unfolded polypeptide to its final, folded, native state (the “picture”).
- COGlory 4y agoYes, it is exactly like that. The objection is a number of people and organisations are talking as if they had solved the recognition problem. The parent commemt was remarking they want to see how a protein folds - it's unlikely that AlphaFold will ever reveal that.