Re:The most important scientific problems have yet to be sol...
by PaulDavisThe1st on Thursday January 09, 2020 @08:20PM
(#22007659)
If I'm filling in the blanks here correctly, what we're still far away from is determining the folded configuration of an arbitrary polypeptide. Is that correct? Or has there been real breakthroughs there? 10 years ago when I last checked in with some folk I knew from EMBL, this still seemed to be a complete pipedream.
Is there a paper that describes the parameters of the peptide structure that go into the "physics do the folding" part? When I was at EMBL, I was focused on using local hydrophobicity to see how predictive it was (not at all). Is the physics model operating at this level, above it, or below it?
The CASP results weren't really a big deal. It was a modest advancement using techniques that were already spreading throughout the community, coupled with a skilled team that understood the score metric very well.
Two state folders can be reversibly folded using empirically determined force fields (two state folders basically go from "any totally unfolded configuration" to "fully folded single structure" in milliseconds); we can just run simulations and let the (quantum-inspired, classically embedded) physics do the folding, or we can use other techniques, like Rosetta (monte carlo plus lots of empirical data from known structures), or evolutionary data-based techniques (like Deepmind and others used).