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Table 7 Optimal scaling factors for the MM/GBSA(+ HB) model obtained averaging over different time intervals. Standard deviations (see Methods section) are given in parentheses.

From: Identification of DNA-binding protein target sequences by physical effective energy functions: free energy analysis of lambda repressor-DNA complexes.

MM/GBSA+(HB) 0.0–0.5 ns 0.5–1.0 ns 0.0–1.0 ns
x Coul 0.052 (0.028) 0.012 (0.024) 0.039 (0.029)
x vdW 0.118 (0.049) -0.039 (0.055) 0.060 (0.064)
x GB 0.054 (0.029) 0.014 (0.025) 0.040 (0.031)
x H -0.001 (0.005) 0.007 (0.005) 0.004 (0.006)
x P -0.013 (0.004) 0.001 (0.004) -0.007 (0.005)
x HP -0.039 (0.120) 0.078 (0.107) 0.027 (0.145)
x const -10.184 (6.002) 3.055 (4.486) -2.953 (6.527)