On Modeling Folding of Proteins

FIGURE 3.11 The lattice protein of Sali et al. [100]. Thin lines indicate the contact term. 

D/D matrix offers good characterization of the degree of folding of such structures. The element i, j) of the D/D matrix is defined as 

12 has been constructed so to fill the 3 x 3 x 3 cube with the maximal number of straight segments in order to explore if so-folded protein represents one of the least folded proteins. 

FIGURE 3.13 Plot of the total energy of conformation against the degree of foldedness of proteins. 

FIGURE 3.14 Illustration of contact interaction graphs for model folded proteins. 

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