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Quantitative comparison of alternative methods for coarse-graining biological networks
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10.1063/1.4812768
/content/aip/journal/jcp/139/12/10.1063/1.4812768
http://aip.metastore.ingenta.com/content/aip/journal/jcp/139/12/10.1063/1.4812768
View: Figures

Figures

Image of FIG. 1.
FIG. 1.

Structures of the 1-residue alanine dipeptide (all-atom), the 35-residue villin headpiece (ribbon), and the 263-residue β-lactamase (ribbon). Structures were drawn with PyMOL.

Image of FIG. 2.
FIG. 2.

The log  of the evidence for coarse-grained models built with different methods. The mean value from 100 bootstrapped samples is reported (bars) with 68% confidence intervals (error bars). Larger (less negative) numbers indicate better results. The large magnitudes are comparable to those found in Refs. and arise from the products of a large number of small probabilities in the likelihood function.

Image of FIG. 3.
FIG. 3.

The overlap between coarse-grained models built with different methods. The mean value from 100 bootstrapped samples is reported. Larger numbers indicate greater similarity.

Image of FIG. 4.
FIG. 4.

The mutual information between coarse-grained models built with different methods. The mean value from 100 bootstrapped samples is reported. Larger numbers indicate greater similarity.

Image of FIG. 5.
FIG. 5.

The metastability of coarse-grained models built with different methods. The mean value from 100 bootstrapped samples is reported (bars) with 68% confidence intervals (error bars).

Image of FIG. 6.
FIG. 6.

The 10 slowest relaxation timescales from the slowest (a) to the fastest (j) for the original villin model before coarse-graining (black) and coarse-grainings from BACE (blue), HNEG (yellow), MPP (green), PCCA+ (red), and PCCA (cyan).

Image of FIG. 7.
FIG. 7.

The interstate flux for the 10 slowest relaxation timescales for each of the villin coarse-grained models. Fluxes were calculated from a transition probability matrix with a lag time of 100 ns based on the apparent leveling off of the relaxation timescales at this lag time (which indicates Markovian behavior ).

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/content/aip/journal/jcp/139/12/10.1063/1.4812768
2013-07-08
2014-04-17
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Quantitative comparison of alternative methods for coarse-graining biological networks
http://aip.metastore.ingenta.com/content/aip/journal/jcp/139/12/10.1063/1.4812768
10.1063/1.4812768
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