Or 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.
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.