A structure-based method for derivation of all-atom potentials for protein folding
Shakhnovich, Eugene I.
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CitationKussell, 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.
AbstractA 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.
Citable link to this pagehttp://nrs.harvard.edu/urn-3:HUL.InstRepos:41534342
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