[ahelwer]

We've known the "why" of protein folding for many years. You can plug your amino acid chain into NWChem and have it spit out the system hamiltonian. From there it's just using the Schrodinger equation to evolve the system in time. Good luck finding a computer that can do that before the universe goes dark, though.

I guess you're hoping for some higher-level heuristic that would let us skip a lot of the computation. Maybe it exists. That isn't how nature does it, though.

[dekhn]

uhhhhh nobody has convincingly shown for sure that applying time-dependent schrodinger to a protein hamiltonian would solve the folding problem, even given infinite computer time. (note that I am one of the few people who has tried using extremely large amounts of computer time and classical force fields)

[ahelwer]

Reading your other comments you say you have a PhD in biophysics so yeah you know a lot more about this than me, so I'm interested - are there reasons to believe it isn't just a matter of scale (obviously we are talking about exponential scaling here aka completely infeasible but you know)? The field of quantum computing has also tied a lot of its value to efficient hamiltonian simulation and what that can do for biology & material science.

[dekhn]

I only mean that nobody has done the experiment (nor is it feasible to run). My base hypothesis is, given enough computer time and an accurate potential function, molecular dynamics indeed would solve the limited protein folding problem (small domains that are soluble in water), but I also think there must be a far simpler and less expensive way to do it (most likely using deep neural nets that incorporate a wide range of information).

That said I also believe that QC in principle could be a way to address this effectively as well, but I'm waiting until I see somebody demonstrate something interesting and useful before I get excited.