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J Mol Biol. 2007 Sep 21;372(3):756-63. Epub 2007 Jul 17.

Folding time predictions from all-atom replica exchange simulations.

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Institute for Molecular Pediatric Sciences and Department of Pediatrics, Gordon Center for Integrative Science, The University of Chicago, Chicago, IL 60637, USA.


We present an approach to predicting the folding time distribution from all-atom replica exchange simulations. This is accomplished by approximating the multidimensional folding process as stochastic reaction-coordinate dynamics for which effective drift velocities and diffusion coefficients are determined from the short-time replica exchange simulations. Our approach is applied to the folding of the second beta-hairpin of the B domain of protein G. The folding time prediction agrees quite well with experimental measurements. Therefore, we have in hand a fast numerical tool for calculating the folding kinetic properties from all-atom "first-principles" models.

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