[momeara]

Hi Chris,

You bring up very good issues and perhaps I'm being too optimistic. I definitely agree that there isn't going to be one single mapping of sequence --> energy landscape any time soon or even ever.

But I think there are subproblems that are easier because the search space is more limited[1] or the chemistry is easier (e.g. avoiding chemical reactions or interactions with high energy fields). I think often the major modeling challenge is identifying when it is feasible to take advantage of problem constraints or when lower levels of theory can be used. For example there are a range of "enhanced sampling methods" for molecular dynamics that e.g. constrain the the simulation to a reaction coordinate or assume Markov transitions between states so they can be computed on a distributed cluster.

Taking advantage of these opportunities often requires a fair amount of engineering to build appropriate representations. I wonder to what extent these representations can be learned?