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Comparison of two adaptive temperature-based replica exchange methods applied to a sharp phase transition of protein unfolding-folding
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10.1063/1.3603964
/content/aip/journal/jcp/134/24/10.1063/1.3603964
http://aip.metastore.ingenta.com/content/aip/journal/jcp/134/24/10.1063/1.3603964

Figures

Image of FIG. 1.
FIG. 1.

(a) Final replica exchange temperature sets at 39 ns. (b) Metropolis exchange rates over the last 20 ns of simulation time. (c) Fraction cold, f(T), as a function of temperature index. (d) Median temperature of all 32 windows as the simulations progressed. Legend: black closed circles – fixed-T ReX, red open squares – EE-ReX, blue closed squares – CM-ReX, green dashed line – ideal f i if current, j, is maximal.

Image of FIG. 2.
FIG. 2.

(a) Progression of predicted unfolding-folding melting temperature (max C p method) as a function of simulation time. (b) Number of replica clients that populate conformations less than 5-Å RMSD from the starting native structure. (c) Heat capacities of the three ReX methods for the last 20 ns. (d) Fraction of folded conformations (RMSD < 5 Å) vs. temperature for the last 20 ns. Legend: same as Fig. 1.

Image of FIG. 3.
FIG. 3.

Potential of mean force landscapes at the predicted T mG fold = 0) in the dimensions of potential energy, E, and C α RMSD for [(a)/(b)] fixed-T ReX, [(c)/(d)] EE-ReX, and [(e)/(f)] CM-ReX. Plots on the right are native basin close-ups of those on the left.

Tables

Generic image for table
Table I.

Comparison of thermodynamic observables between the predictions from the three different ReX methods (using the last 20 ns) and the experiment. (See Ref. 19.) Uncertainty for simulation observables estimated as the standard deviation of 5-ns block averages.

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/content/aip/journal/jcp/134/24/10.1063/1.3603964
2011-06-28
2014-04-16
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Comparison of two adaptive temperature-based replica exchange methods applied to a sharp phase transition of protein unfolding-folding
http://aip.metastore.ingenta.com/content/aip/journal/jcp/134/24/10.1063/1.3603964
10.1063/1.3603964
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