Not Nature but Molecular Systems Biology [2], apologies, in the context of reverse docking for antibiotics discovery:
"We confirm extensive promiscuity, but find that the average area under the receiver operating characteristic curve (auROC) is 0.48, indicating weak model performance."
Derek Lowe had a post about this earlier this month [1] (which includes important qualifications I failed to omit).
[1] "Benchmarking AlphaFold-enabled molecular docking predictions for antibiotic discovery", Molecular Systems Biology 2022 18:e11081 https://doi.org/10.15252/msb.202211081
This is already known. Structural models are usually not well suited for protein-ligand docking, where proper pocket modelling and accurate side chain positioning are key for the determination of true positive hits.
Sorry, you don't know what you're talking about. Nobody is truly claiming these models can be used directly for drug discovery (well, some people claim that; but they're wrong). We already knew that, though- the same problem exists with high quality crystal structures.
What would be more interesting is if we did a whole bunch of crystal or cryo-EM structures far from what we've previously determined and demonstrate whether alphafold could make out-of-class predictions for them.
