Hey,
so this question has probably be asked many times, but since I could not search the forum, i will ask again:

I guess you assume the lowest energy configurations are the actual configurations the proteins have.
Can we really assume that? Why could it not be that nature runs into a local minimum? Probably a god way to somehow check this, is to use proteins with a known structure and see if you can get a lower energy configuration. I would like to know, if you tried this and what the outcome was.
Thank you for your help!

Frank Schwemmer