A structure-based method for derivation of all-atom potentials for protein folding

Edo Kussell, Jun Shimada, Eugene I. Shakhnovich

Research output: Contribution to journalArticlepeer-review


A 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 Cα distance rms from the native structure of less than 2 Å. 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.

Original languageEnglish (US)
Pages (from-to)5343-5348
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Issue number8
StatePublished - Apr 16 2002

ASJC Scopus subject areas

  • General


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