High-resolution protein folding with a transferable potential

@article{citeulike:494752, abstract = {A 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 {approx}3 A 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.}, author = {Hubner, Isaac A. and Deeds, Eric J. and Shakhnovich, Eugene I. }, citeulike-article-id = {494752}, journal = {PNAS}, keywords = {ab-initio, biophysics, protein\_structure, structure\_prediction}, month = {December}, number = {52}, pages = {18914--18919}, posted-at = {2006-02-07 02:17:31}, priority = {2}, title = {High-resolution protein folding with a transferable potential}, url = {http://www.pnas.org/cgi/content/abstract/102/52/18914}, volume = {102}, year = {2005} }

TY - JOUR ID - citeulike:494752 L3 - citeulike-article-id:494752 TI - High-resolution protein folding with a transferable potential JF - PNAS VL - 102 IS - 52 SP - 18914 EP - 18919 N2 - A 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 {approx}3 A 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. KW - ab-initio KW - biophysics KW - protein_structure KW - structure_prediction AU - Hubner, Isaac AU - Deeds, Eric AU - Shakhnovich, Eugene PY - 2005/12/27/ UR - http://www.pnas.org/cgi/content/abstract/102/52/18914 ER -