Would you consider switching your interest to protein structure prediction? In particular, the current most advanced model is a closed-source, closed-weights system that was trained on a proprietary hardware. It is intentionally kept that way for now to enable deepmind to commercialize their product.

The goal here isn't to make the best performing model: it's ablation. How much can we remove from protein structure prediction (such as multiple sequence alignments and molecular dynamics, which were two improvements in AF3), while still having a generalized model that can predict novel folds.

Then focus on teaching the minimal necessary math and code to reproduce the results to the larger biological community. All I can say about AF3 is that it literally taught me that everything I learned about protein structure prediction in the last 30 years was misguided, or outright wrong.

Don't worry about drug discovery or any of the hard stuff. Just continue to show that all that's required to predict novel structures is the existing PDB.