I think you have this backwards in practice. It was in the 80s that I first read a paper about a de-novo protein design engineered for a specific stable conformation. Natural proteins have no reason to be particularly predictable, just as genetic programming produces hard-to-understand programs relative to human-written ones. In fact making the structure especially stable against perturbations seems like it'd make it less responsive to changing evolutionary pressures.
The forward folding problem lets you determine structures from a known genetic sequence. So for example you could very quickly sequence the genome of a virus and figure out how it worked much faster than current methods allow.
The reverse folding problem lets you specify a structure and then make a genetic sequence to produce it. For example you could look at this virus to see how it infects its host, then design a custom protein to act as an anti-body stopping it, which is a capability we don't currently have.
Forward folding is certainly useful, but reverse folding would be revolutionary.
The set of all proteins which can potentially be expressed in an organism is known. Now maybe we also get decent (static) structure information for these. But the interaction of a virus with the host cell is much more complex. There is much more than just an amino acid sequence involved. And these parts are all moving, so a static picture as we now can create faster than before does not contain all the information necessary to fully understand the functions.
No, the genome of the host is much smaller than the theoretical number of combinations. There are about 20 to 30k different proteins in a human cell (about 20k directly encoded on the DNA).
Right, but you made the example with the virus docking at a known organism. If you do synthetic biology and modify bacteria to produce any proteins then the situation is different of course.
The other comment mentioned the example of making proteins that bind a structure. Heres an extension - a general understanding of how an enzyme works to catalyze chemical reactions, is that it binds the reaction intermediate with higher affinity than the two substrates; thus if we have this reverse ability, we can start inventing enzymes that can catalyze any arbitrary chemical reaction, even ones that need energy input, so you could imagine for example enzyme systems that can convert plastic to fuel!
Ok, then this is about enzymes which do not yet exist in the organism. You could then modify bacteria so they produce this enzyme and feed on plastic, I see.
But producing fuel as the fellow suggested would then be another function to be added to the bacterium; and maybe it should work on different kinds of plastic.
Of course, that's why I focused on degradation. There's plenty of room for improvement. For instance, PETase is not very efficient actually, and many research groups are working on its engineering.
