Elevator pitch summary: View and manipulate energy so geometry becomes a side-effect.
The game is beautifully executed and ingenious. And frustrating but that is just a side-effect of reality. As I explore this system, I wonder about something. I am reaching here and it may be a dead end but might be worth thinking about. Also it may seem interesting to me just because I am ignorant.
The entire picture is built around spatial representation of the proteins. But the spatial realization of the energy state of the protein is just a side-effect of its energy state. This spatial bias also affects the methods of control and manipulation. Its drawback becomes apparent when very small changes in the geometry result in very large swings in the score.
Is there a natural, sensible way of visualizing and manipulating the energy states of the protein, and segments of it and its environment? Like a potential field defined on the elements of the sequence. Like letting the 20th element of the chain see the field in the vicinity of the 43rd element. I hope that small changes in the energy in a certain part of the chain would, for the most part, lead to small changes in the overall state and that gradients in the potential field would become apparent as drivers of change.