This is a key but secondary concern to many of us working in molecular geneticist who will use AlphaFold 3 to evaluate pair-wise interactions. We often have genetic support for an interaction between proteins A and B. For example, in a study of genetic variation in responses of mice to morphine I currently have two candidate proteins that interact epistatically, suggesting a possible “lock and key” model—-the mu opiate receptor (MOR) and FGF12. I can now evaluate the likelihood of a direct molecular interaction between these proteins and possible amino acids substitutions that account for individuals difference.

In other words I bring a hypothesis to AF3 and ask for it to refute or affirm.