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AMB Express

Table 1 The average values of SASA, VDW energies and the average number of protein-protein (intramolecular) and protein-solvent H-bonds in 1URX and 3WZ1 at different temperatures

From: Thermostability mechanisms of β-agarase by analyzing its structure through molecular dynamics simulation

 

300 K

400 K

500 K

1URX

 RMSD

1.34

2.47

3.94

 RMSF

1.27

2.10

3.55

 SASA

109.33

130.17

190.38

 Protein–protein H-bond

69.94

54.55

45.88

 Protein-solvent H-bond

199.77

145.02

97.32

 VDW-force (protein)

− 1072.66

− 924.63

− 717.41

 VDW-force (protein-water)

− 459.07

− 427.31

− 394.84

3WZ1

 RMSD

1.80

1.97

4.74

 RMSF

3.19

1.96

4.22

 SASA

120.91

146.69

209.96

 Protein–protein H-bond

76.83

61.18

47.85

 Protein-solvent H-bond

216.39

155.81

112.68

 VDW-force (protein)

− 1027.51

− 875.258

− 662.48

 VDW-force (protein-water)

− 474.68

− 418.29

− 426.44

  1. SASA, H-bonds, VDW-force denote solvent accessible surface area, hydrogen bonds and Van Der Waals force, respectively. The values of SASA and VDW-force are given in Å and kcal/mol respectively
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