DM didn't "solve" anything around proteins. They just made an improvement to existing homology modelling methods. If you look, the system is incredibly dependent on having large numbers of high quality sequence alignments to proteins with known structure and lots and lots of evolutionary data.

This was actually fairly obvious 20 years ago and it's been disappointing to me to see how long it took somebody to make this improvement, but really, it couldn't have been done without recent algorithmic improvements and huge amounts of CPU time.