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Table 6 Window score based on residue surface areas

From: Can molecular dynamics simulations help in discriminating correct from erroneous protein 3D models?

  Sequence   E57 F58 E59 I60 Y61 Y62 I63 L64 L65 G66 E67
t = 0 Win. score -2.61 -2.38 -2.15 -2.48 -2.36 -2.84 -2.74 -2.53 -2.45 -2.57 -2.50  
  Ind. score -1.88 -3.06 -3.23 -1.36 -2.81 -4.72 -0.97 -2.34 -4.19 -0.69 -5.99  
t = 280 Win. score -1.23 -1.18 -1.18 -1.26 -1.21 -1.28 -1.25 -1.21 -1.37 -1.44 -1.33  
  Ind. score -0.95 -1.61 -0.67 -1.03 -1.38 -0.09 -0.93 -2.76 -2.52 -0.69 -1.37  
Query Win. score -1.47 -1.34 -1.36 -1.48 -1.48 -1.50 -1.46 -1.50 -1.00 -0.99 -1.20  
  Ind. score -1.09 -1.10 -5.99 -0.82 -0.18 -1.18 -0.58 -1.07 -2.92 -0.69 -0.87  
  1. Residue window centred at Tyr62. Ind score is the individual score for the residue; Win. score is the window score, i.e., the mean of the individual scores in a window of 11 residues centred at the residue of interest. The first 2 lines, labelled t = 0, correspond to the minimised initial conformation at t = 0 ps; the next 2 lines, labelled t = 280, correspond to the minimised conformation along the MD trajectory at 400 K that has the smallest value for the Tyr 62 window score (t = 280 ps snapshot); the last two lines, labelled query, correspond to the score values of the residues in their native structure for comparison purpose. Residues in bold are shown in Fig. 8