I agree. "AlphaFold achieves a median score of 87.0 GDT". While this is a major advance, to me 100 GDT would be 'solved', not 87.
Are you a domain expert? Because:
> According to Professor Moult, a score of around 90 GDT is informally considered to be competitive with results obtained from experimental methods.
What would be informatively useful would be to know how much accuracy is needed on average for drug engineers, I'd say that 99% is more likely to be the minimum to make solid inferences
I might be missing something here, but isn't "experimental methods" just shorthand for "our best knowledge of a protein's structure, obtained via NMR or X-ray crystallography"? In that case, I'm not sure what "solving" protein folding even means - literally zero mean error? We can't know/solve anything beyond our best knowledge, that's tautological.
> What would be informatively useful would be to know how much accuracy is needed on average for drug engineers.
Yeah that would be interesting, but:
> I'd say that 99% is more likely to be the minimum to make solid inferences
...what are you basing this on?
"We can't know/solve anything beyond our best knowledge, that's tautological." yes it is indeed tautological if you assume that experimental methods can't get better then guess what? It follows that they can't get better!
"what are you basing this on?" on nothing solid, that's why I say it would be interesting. 99% is a non negligible error rate given that proteins have generally a not very high atom count and they the protein will be produced an enormous amount of time, then the 1% error progagate and can a priori easily break the system. But this guess is not solid as I'm not an expert. 99% accuracy for simple (low atom count) proteins is a sensitive error and could be negligible for very high atom count proteins.
That's not clear at all, because perfect measurement doesn't exist. I agree that improving is always a worthy goal, but clearly we don't need 100% accuracy to consider something "solved" for the purposes of science. Also, "3D structure" of a protein is not a fixed truth, the parts are in motion all the time and may even have multiple semi-stable conformations. Rather than focusing on X,Y,Z perfection, I would imagine getting the angles between bonds, or the general topological conformation right would be more valuable.
> if you assume that experimental methods can't get better ...
I'm saying that if your definition for "solved" is "perfect knowledge", then we might as well not discuss whether method X or Y solves the problem, because they obviously do not.
The more I think about it, the more I think we should just drop the whole debate over the word "solved". Clearly different experiments and different proteins will have different requirements which may or may not be met by this or by other techniques - I agree that I would be interested to hear an expert weigh in on those requirements.