I don't think anybody is 100% certain that doing a full quantum simulation of a protein (in a box of water) would recapitulate the dynamics of protein folding. It seems like a totally reasonable claim, but one that could not really be evaluated.
If you have a paper that makes a strong argument around this claim, I'd love to see it. BTW- regarding folding funnels, I learned protein folding from Ken Dill as a grad student in biophysics at UCSF, and used to run MD simulations of nucleic acids and proteins. I don't think anybody in the field wants to waste the time worrying about running full quantum simulations of protein folding, it would be prohibitevly expensive even with far better QM simulators than we have now (IE, n squared or better).
Also the article you linked- they are trying to find the optimal structure (called fold by some in the field). That's not protein folding- it's ground state de novo structure prediction. Protein folding is the process by which an unfolded protein adopts the structured state, and most proteins don't actually adopt some single static structure but tend to interconvert between several different substructes that are all kinetically accessible.
> I don't think anybody is 100% certain that doing a full quantum simulation of a protein (in a box of water) would recapitulate the dynamics of protein folding.
True, until it's experimentally shown there's still some possibility QM wouldn't suffice. Though I've not read anything that'd give reason to believe QM couldn't capture the dynamic behavior of folding, unlike the uncertainty around dark matter or quantum supremacy or quantum gravity.
Though it might be practically impossible to setup a simulation using QM which could faithfully capture true protein folding. That seems more likely.
> It seems like a totally reasonable claim, but one that could not really be evaluated.
If quantum supremeacy holds, my hunch would be that it would be feasible to evaluate it one day.
The paper I linked was mostly to showcase that there seem to be approaches utilizing quantum computing to speed up solving QM simulations. We're still in the early days of quantum computing algorithms and it's unclear what's possible yet. Tackling a dynamic system like a unfolded protein folding is certainly a ways away though!
> Also the article you linked- they are trying to find the optimal structure (called fold by some in the field). That's not protein folding- it's ground state de novo structure prediction.
Thanks! I haven't worked on quantum chemistry for many years, and only tangentially on protein folding, so useful to know the terminology. The meta table states and that whole possibility of folding states / pathways / etc fascinates me as potentially being emergent property of protein folding physics and biology as we know it.
If you have a paper that makes a strong argument around this claim, I'd love to see it. BTW- regarding folding funnels, I learned protein folding from Ken Dill as a grad student in biophysics at UCSF, and used to run MD simulations of nucleic acids and proteins. I don't think anybody in the field wants to waste the time worrying about running full quantum simulations of protein folding, it would be prohibitevly expensive even with far better QM simulators than we have now (IE, n squared or better).
Also the article you linked- they are trying to find the optimal structure (called fold by some in the field). That's not protein folding- it's ground state de novo structure prediction. Protein folding is the process by which an unfolded protein adopts the structured state, and most proteins don't actually adopt some single static structure but tend to interconvert between several different substructes that are all kinetically accessible.