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Combinatorial design of protein sequences with applications to lattice and real proteins
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10.1063/1.3236519
/content/aip/journal/jcp/131/12/10.1063/1.3236519
http://aip.metastore.ingenta.com/content/aip/journal/jcp/131/12/10.1063/1.3236519
View: Figures

Figures

Image of FIG. 1.
FIG. 1.

Left figure shows the plot of vs and right figure shows the plot of vs . The solid blue lines represent the theory results and the red circles denote the exact enumeration results.

Image of FIG. 2.
FIG. 2.

Left figure shows the plot of vs and right figure shows the plot of vs . The blue squares represent the theory results and the red triangles denote the exact enumeration results.

Image of FIG. 3.
FIG. 3.

The number of competing conformations (see text) vs folded state energy for four designed sequences corresponding to four different . For the energy gap . Hence all the conformations are equivalent and no distinct native state is identified at . For rest of the sequences distinct native state is observed.

Image of FIG. 4.
FIG. 4.

Contour plot to show the variation of sequence entropy(s) and fraction of sequence hydrophobic composition with foldability criteria .

Image of FIG. 5.
FIG. 5.

(a) Variation of with sequence positions (i) at . (b) Variation of with sequence positions (i) at . Blank black bars denote exact enumeration results and solid blue bars present theoretical results.

Image of FIG. 6.
FIG. 6.

(a) Variation of with sequence positions (i) at . (b) Variation of with sequence positions (i) at . Blank black bars denote exact enumeration results and solid blue bars present theoretical results.

Image of FIG. 7.
FIG. 7.

(a) Variation of at over all possible pairs of site 1. (b) Variation of at over all possible pairs of site 1. Blank black bars denote exact enumeration results and solid blue bars represent theoretical results.

Image of FIG. 8.
FIG. 8.

(a) Variation of at over all possible pairs of site 1. (b) Variation of at over all possible pairs of site 1. Blank black bars denote exact enumeration results and solid blue bars represent theoretical results.

Image of FIG. 9.
FIG. 9.

Left figure shows the plots of substitution dependency pattern at various sites for foldability criteria and right figure represents the substitution dependency plots for .

Image of FIG. 10.
FIG. 10.

Comparison of observed and theoretically obtained sequence variability in terms of . The target structure is the protein conformation and the corresponding . The inset graph is shown to compare the correlation between the observed and theory results. The corresponding correlation coefficients are given by value.

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/content/aip/journal/jcp/131/12/10.1063/1.3236519
2009-09-23
2014-04-19
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Combinatorial design of protein sequences with applications to lattice and real proteins
http://aip.metastore.ingenta.com/content/aip/journal/jcp/131/12/10.1063/1.3236519
10.1063/1.3236519
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