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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)