There are a lot of approaches, and they do not all require a brute force simulation. Nature herself seems to have a library of functional domains from which sh

There are a lot of approaches, and they do not all require a brute force simulation. Nature herself seems to have a library of functional domains from which she can mix and match to produce a larger mechanical device - in addition to the atomic resolution mutations, and tertiary structural features. There are a lot of very useful ways people do design proteins right now that do not involve structural prediction. Further, very much unlike the digital sciences, a gigantic library of parts, functions, routines and 'example code' already exist. If you want a piece of nano-technology that does X, just go look for an organism that lives in a condition where X is useful - and in there genome it will be. We have a huge pile of hyper-advanced alien source code that we can dig through. We don't have to reinvent it all on our own.