Kussell, EdoShimada, JunShakhnovich, Eugene I.2019-10-112002Kussell, E., J. Shimada, and E. I. Shakhnovich. 2002. “A Structure-Based Method for Derivation of All-Atom Potentials for Protein Folding.” Proceedings of the National Academy of Sciences99 (8): 5343–48. https://doi.org/10.1073/pnas.072665799.0027-84240744-28311091-6490http://nrs.harvard.edu/urn-3:HUL.InstRepos:41534342A method for deriving all-atom protein folding potentials is presented and tested on a three-helix bundle protein, as well as on hairpin and helical sequences. The potentials obtained are composed of a contact term between pairs of atoms, and a local density term for each atom, mimicking solvent exposure preferences. Using this potential in an all-atom protein folding simulation, we repeatedly folded the three-helix bundle, with the lowest energy conformations having a C-alpha distance rms from the native structure of less than 2 A. Similar results were obtained for the hairpin and helices by using different potentials. We derived potentials for several different proteins and found a high correlation between the derived parameters, suggesting that a potential of this form eventually could be found that folds multiple, unrelated proteins at the atomic level of detail.en-USJournal Article2019-10-1110.1073/pnas.072665799