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Table 4 Optimal scaling factors for the MM/GBSA model and the MM/GBSA(+HB) model: analysis of the λ repressor-operator system (λ), of the Cro-operator system (Cro) and the joint analysis (λ + Cro). 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 λ Cro λ + Cro
x Coul 0.157 (0.045) 0.132 (0.067) 0.153 (0.037)
x vdW 0.252 (0.124) 0.332 (0.132) 0.313 (0.086)
x GB 0.142 (0.046) 0.121 (0.069) 0.145 (0.038)
x P -0.010 (0.012) 0.019 (0.012) -0.009 (0.006)
x H -0.029 (0.008) -0.009 (0.011) -0.031 (0.005)
x const -11.744 (28.025) 70.791 (37.615) -19.519(11.903)
MM/GBSA(+HB) λ Cro λ + Cro
x Coul 0.042 (0.053) 0.016 (0.066) 0.051 (0.041)
x vdW 0.206 (0.113) 0.219 (0.118) 0.262 (0.079)
x GB 0.025 (0.054) 0.002 (0.068) 0.043 (0.041)
x P -0.016 (0.011) -0.001 (0.012) -0.024 (0.006)
x H -0.023 (0.008) -0.005 (0.010) -0.029 (0.005)
x HB -0.533 (0.156) -0.879 (0.224) -0.561 (0.125)
x const 13.699 (26.308) 65.011 (32.867) -21.595 (10.908)