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. 2011 Dec 16;11:361. doi: 10.1186/1471-2148-11-361

Table 1.

The protein-like properties of sequence evolution over simulation time is shown

Simulation time Model Core Surface Gamma Support Shape Parameter
Hydrophobicity Hydrophobicity
(%) (%)
5000 Informational 39.7 11.2 0.35 0.02

25000 Informational 42.1 15.2 0.72 0.95

50000 Informational 42.9 18.5 0.72 1.46

70000 Informational 45.0 20.4 0.69 1.55

100000 Informational 47.4 23.0 0.73 2.07

150000 Informational 47.7 27.7 0.49 2.61

200000 Informational 49.6 30.5 0.12 2.73

5000 Physics-based 83.4 49.2 0.20 3.31

25000 Physics-based 82.8 49.5 0.37 2.58

50000 Physics-based 81.7 49.1 0.31 2.06

70000 Physics-based 81.7 48.4 0.61 1.86

100000 Physics-based 81.1 48.6 0.09 1.87

150000 Physics-based 81.6 48.2 0.25 1.76

200000 Physics-based 81.1 48.0 0.10 1.88

Simulation time is listed in generations. Core and surface hydrophobicities shown reflect the population average percentage of hydrophobic residues in buried and exposed positions. Gamma support indicates the fractional support for a model including a gamma distribution of rates, and the shape parameter shows the α value of such a distribution.