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Are AlphaFold's new results a miracle?

So this happened: DeepMind (with 48 authors, including a new member of the British nobility) decided to compete with me. Or rather, with some of my work from 10+ years ago. Apparently, AlphaFold 3 can now predict how any drug-like molecule will bind to its target protein. And it does so better than AutoDock Vina (the most cited molecular docking program, which I built):

Oftentimes, they take baby steps, choosing to study drug-like molecules similar to the ones already discovered for the same or related targets. Long ago, when I was a PhD student at Columbia, I trained a neural network to predict protein flexibility. If AlphaFold 3 is actually learning any non-obvious insights from data, about how molecules interact, why is it missing possibly the most obvious one of them all, which is that interpenetrating atoms are bad?

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