Machine learning typically uses existing data to predict new data. Please explain: Does it mean that AlphaFold can only use known types of interactions between atoms and will mispredict the structure of proteins that use not yet known interactions?
And why we cannot just simulate protein behaviour and interactions using quantum mechanics?
QM calculations have been done in proteins, but they’re computationally very expensive. IIRC, there are hybrid approaches where only a small portion of interest in the protein structure is modelled by QM and the rest by classical molecular mechanics.