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Scientists can verify that an AlphaFold-predicted structure is correct, or at least useful, without being able to get the structure experimentally. For instance
by comicjk 6y ago
Scientists can verify that an AlphaFold-predicted structure is correct, or at least useful, without being able to get the structure experimentally. For instance, we could use the AlphaFold-predicted structure to do protein-ligand binding calculations for a bunch of known molecules. If these calculations agree with experimental protein-ligand binding (which they generally do for proteins with known structures), then we can say with high confidence that we've got a good structure.
- dontbeevil1992 6y agodoes that mean that protein-folding is sort of in NP?
- dekhn 6y agoThe way computer scientists do it, yes, it is. In the CS situation you define an energy function (in this case representing the physical behavior of the protein in water) and find a heuristic to approximate the coordinates of the lowest energy configuration; done, problem solved. in reality, that's not how it works at all. The energy functions we have are crappy and require too much sampling before we can find the lowest energy configuration. And more importantly, it doesn't look like proteins typically fold to their lowest energy configuration (with the exception of some small fast two state folders), but rather explore a kinetically accessible region around there (or even somewhere else entirely, if the energy cost to transition is too high). Methods like AF depend heavily on large amount of information correlation from evolutionary data, which has historically been of the highest value for making decisions about protein structure.
- hedora 6y agoIt’s probably not in NP, in that there is not a polynomial time algorithm that checks solutions for correctness.