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It's not either-or, it's yes-and. We don't have to abandon one for the other. AlphaFold 3 can rapidly reduce a vast search space in a way physically-based met
by panarky 2y ago
It's not either-or, it's yes-and. We don't have to abandon one for the other.
AlphaFold 3 can rapidly reduce a vast search space in a way physically-based methods alone cannot. This narrowly focused search space allows scientists to apply their rigorous, explainable, physical methods, which are slow and expensive, to a small set of promising alternatives. This accelerates drug discovery and uncovers insights that would otherwise be too costly or time-consuming.
The future of science isn't about AI versus traditional methods, but about their intelligent integration.
- nextos 2y agoOr you can treat AlphaFold as a black box / oracle and work at systems biology level, i.e. at pathway and cellular level. Protein structures and interactions are always going to be hard to predict with interpretable models, which I also prefer. My only worry is that AlphaFold and others, e.g. ESM, seem to be bit fragile for out-of-distribution sequences. They are not doing a great job with unusual sequences, at least in my experience. But hopefully they will improve and provide better uncertainty measures.