Hrmm, I think I was expecting a different type of disagreement when you said he was wrong on facts.
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.
If you can discover a drug faster and that drug is as useful as dirt does it matter?
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.
you just described how modern high content screening, which has been one of the most useful techniques for finding drug leads, works. Since lead-finding is a bottleneck in the drug discovery process, it has been highly effective because it can measure things that are not currently computationally accessible.