Hubner, Isaac A.Deeds, Eric J.Shakhnovich, Eugene I.2019-10-112005Hubner, I. A., E. J. Deeds, and E. I. Shakhnovich. 2005. “High-Resolution Protein Folding with a Transferable Potential.” Proceedings of the National Academy of Sciences102 (52): 18914–19. https://doi.org/10.1073/pnas.0502181102.0027-84240744-28311091-6490http://nrs.harvard.edu/urn-3:HUL.InstRepos:41534317A generalized computational method for folding proteins with a fully transferable potential and geometrically realistic all-atom model is presented and tested on seven helix bundle proteins. The protocol, which includes graph-theoretical analysis of the ensemble of resulting folded conformations, was systematically applied and consistently produced structure predictions of approximate to 3 angstrom without any knowledge of the native state. To measure and understand the significance of the results, extensive control simulations were conducted. Graph theoretic analysis provides a means for systematically identifying the native fold and provides physical insight, conceptually linking the results to modern theoretical views of protein folding. In addition to presenting a method for prediction of structure and folding mechanism, our model suggests that an accurate all-atom amino acid representation coupled with a physically reasonable atomic interaction potential and hydrogen bonding are essential features for a realistic protein model.en-USJournal Article2019-10-1110.1073/pnas.0502181102