I'm sure you know your stuff, and that you have a lot of experience with proteins that haven't helped with drug discovery or engineering, but it sounds like this is indeed a mismatch between predictions rather than facts.
It very well could be the case that speeding up certain problems by multiple orders of magnitude really does help with drug discovery, and this isn't factually inconsistent with the fact that solving those problems hasn't turned out to be useful so far in this area.
This isn't my field but I could grab a bunch of random jars off a shelf and pour them into capsules. No matter how fast I can do this won't improve medical outcomes for patients.
Wasn't your claim that the AI process hasn't been shown to generate a useful drug [1]?
Given that improved structures has sped up drug discovery, I can see where the mistake is made (X has improved Y, therefore X will improve Y)
When is “improved structure prediction” useful or important?
Often a process is simplified or distilled down to a sound bite for the general population. Then we simply repeat without understanding the details.
THe problem is those distilled soundbites get learned by the next generation and they try to apply it. At least I will give AlphaFold/DM credit for correcting their language - originally they claimed AF solved protein folding, but really, it's just a structure predictor, which is an entirely different area. Unfortunately, people basically taught computer scientists that the Anfinsen Dogma was truth. I fell for this for many years.
> It states that, at least for a small globular protein in its standard physiological environment, the native structure is determined only by the protein's amino acid sequence.
Seems like "no true scotsman". If you present a counter example, they'll go "but this is only true for "small", the one you gave me isn't small.
Do you say "we're going to give you a problem that is unsolved but likely has a general solution, and you have a chance of making progress, publishing, and moving on to a postdoc" or do you say "THis is an impossibly hard problem and you will only make a marginal improvement on the state of the art because the problem space is so complex and large"?
You say the first because it gets the students interested and working on the problem, only to learn many years later that the simplified model presented was so simplified it wasn't helpful. I fell for that and spent years working on drug discovery, structure prediction, etc, only to realize: while what Anfinsen said was true, it only applies to about 1% of protein space. It's not so much a "no true scotsman" as "some scotsmen wear quilts, and others have beards, but neither of those is sufficient to classify an example as scots".