I like the starter puzzles but I didn't learn much with them. They were too easy or too hard with little learned towards making progress with a big ole protein. How about some very simple proteins to start with in a playground to get used to the physics. For example, 5 or 6 amino acids. The playground concept might be an experience as follows:
Every action taken triggers a popup message that explains a bit about what is happening from a physics perspective. For example, if you click an AA and it rotates, tell the user why it rotated. If the user drags the chain around and the physics engine does someting like pushes the chain apart as a response, explain why it took this action.
Just some thoughts off the top of my head. Having some idea of the biochem, physics and objectives I'm a little more patient but I can imagine newbies getting very frustrated with this "game" and walking away from it. To get people hooked they need to be eased into things very slowly if possible which means a disproportionate amount of work on the introductory puzzles.