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Dominant reaction pathways in protein folding: A direct validation against molecular dynamics simulations
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10.1063/1.3459097
/content/aip/journal/jcp/133/4/10.1063/1.3459097
http://aip.metastore.ingenta.com/content/aip/journal/jcp/133/4/10.1063/1.3459097
View: Figures

Figures

Image of FIG. 1.
FIG. 1.

Left panel: the 16-residue C-terminus of protein G-B1 (PDB code 2gb1). Right panel: its coarse-grained representation used in the present study.

Image of FIG. 2.
FIG. 2.

Typical evolution of the HJ action during the numerical minimization based on the simulated annealing algorithm.

Image of FIG. 3.
FIG. 3.

Time evolution of the fraction of native contacts in a MD simulation based on the coarse-grained model used in this work, at temperatures and .

Image of FIG. 4.
FIG. 4.

Our calculated dominant folding paths and MD folding trajectories, projected on the plane selected by pairs of order parameters. The shaded area denotes the native region.

Image of FIG. 5.
FIG. 5.

Time evolution of the mean-value of the order parameters (left panel), (center panel), and (right panel) during the folding reaction. Squares (circles) represent the result of averaging over DRP (MD) folding trajectories, respectively. The dotted lines represent the time evolution of the order parameters in a typical folding trajectory obtained by MD.

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/content/aip/journal/jcp/133/4/10.1063/1.3459097
2010-07-29
2014-04-17
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Dominant reaction pathways in protein folding: A direct validation against molecular dynamics simulations
http://aip.metastore.ingenta.com/content/aip/journal/jcp/133/4/10.1063/1.3459097
10.1063/1.3459097
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