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Table 1 Optimal scaling factors for the MM/DDDC-OONS model and the MM/DDDC-HP model. 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/DDDC-OONS 1r 2r 4r 8r
x vdW 0.075 (0.071) 0.041 (0.100) 0.043 (0.111) 0.025 (0.116)
x DDDC 0.083 (0.019) 0.184 (0.037) 0.359 (0.076) 0.802 (0.159)
x OONS 0.072 (0.070) -0.020 (0.075) -0.084 (0.061) -0.043 (0.076)
x const 65.254 (20.806) 73.523 (21.615) 75.782 (23.697) 64.715 (26.116)
MM/DDDC-OONS (+HB) 1r 2r 4r 8r
x vdW 0.075 (0.072) 0.040 (0.100) 0.042 (0.109) 0.034 (0.113)
x DDDC 0.068 (0.030) 0.154 (0.046) 0.286 (0.089) 0.637 (0.179)
x OONS 0.075 (0.071) -0.019 (0.075) -0.066 (0.061) -0.010 (0.076)
x HB -0.151 (0.249) -0.166 (0.152) -0.226 (0.145) -0.269 (0.144)
x const 57.867 (24.223) 68.819 (21.992) 69.397 (23.718) 58.463 (25.680)
MM/DDDC-HP 1r 2r 4r 8r
x vdW 0.144 (0.065) 0.215 (0.106) 0.085 (0.115) 0.133 (0.128)
x DDDC 0.076 (0.017) 0.221 (0.033) 0.402 (0.075) 0.844 (0.153)
x P -0.018 (0.008) -0.027 (0.011) -0.007 (0.011) -0.012 (0.012)
x H -0.028 (0.007) -0.021 (0.007) -0.013 (0.008) -0.015 (0.008)
x const -4.023 (26.223) 21.075 (24.822) 38.294 (32.091) 31.927 (29.069)
MM/DDDC-HP + (HB) 1r 2r 4r 8r
x vdW 0.144 (0.065) 0.221 (0.104) 0.105 (0.111) 0.175 (0.123)
x DDDC 0.059 (0.027) 0.185 (0.040) 0.281 (0.089) 0.623 (0.172)
x P -0.018 (0.008) -0.029 (0.011) -0.011 (0.011) -0.018 (0.011)
x H -0.029 (0.007) -0.022 (0.007) -0.017 (0.008) -0.017 (0.007)
x HB -0.181 (0.218) -0.210 (0.138) -0.327 (0.143) -0.332 (0.137)
x const -13.355 (28.624) 12.784 (25.076) 21.219 (31.635) 20.937 (28.041)