Folding proteins by first-passage-times-optimized replica exchange
Document Type
Article
Publication Date
12-1-2008
Abstract
Replica exchange simulations have become the method of choice in computational protein science, but they still often do not allow an efficient sampling of low-energy protein configurations. Here, we reconstruct replica flow in the temperature ladder from first passage times and use it for temperature optimization, thereby maximizing sampling. The method is applied in simulations of folding thermodynamics for a number of proteins starting from the pentapeptide Met-enkephalin, through the 36-residue HP-36, up to the 67-residue protein GS- α3 W. © 2008 The American Physical Society.
Publication Title
Physical Review E - Statistical, Nonlinear, and Soft Matter Physics
Recommended Citation
Nadler, W.,
Meinke, J.,
&
Hansmann, U.
(2008).
Folding proteins by first-passage-times-optimized replica exchange.
Physical Review E - Statistical, Nonlinear, and Soft Matter Physics,
78(6).
http://doi.org/10.1103/PhysRevE.78.061905
Retrieved from: https://digitalcommons.mtu.edu/michigantech-p/10079