Dunno. It's a tool to try to figure the shape of molecules in a similar way that a cryo-electron microscope is a tool for that. Not the end of science imho.
There are things so complex in science that a human mind can never understand them, but a large neural network can.
For some definition of 'understanding'.
Conjecture, that. Even if true I think it will be very hard to find any definition of science along the lines of "training deep neural nets to do the understanding in our stead".
It was big blind luck that the laws of planetary motion turned out to be so simple. There's no reason to think that protein folding can similarly be reduced to some elegant description without needing large blackbox models.
Science is just a methodology to test hypothesis. It does not matter how you get the result as long as the result is empirically scrutinized.