An effective approach for generating a three-Cys2His2 zinc-finger-DNA complex model by docking

BMC Bioinformatics

Table 1 The 10 best Zif268-DNA complex models for each AIR set were selected on the basis of HADDOCK score. Standard deviations are shown as subscripts.

AIR Set	Wrap-around^a conformation	iRMSD^b (Å)	iRMSD^c (Å)	HADDOCK score^d	E_inter^e (kcal mol^-1)	BSA^f (Å²)	F_nat^g
(i)	50/200	2.22_0.34	7.19_3.84	-241.91_6.39	-1012.96_44.52	2797.64_72.76	0.71_0.05
(ii)	56/200	2.62_0.27	6.84_2.59	-189.02_13.76	-820.31_56.69	2428.23_98.19	0.58_0.03
(iii)	200/200	2.14_0.27	2.28_0.20	-238.62_4.54	-999.27_35.34	2780.30_103.50	0.72_0.04

^aNumber of wrap-around models from analysis of 200 complex models.
^binterface Root Mean Square Deviation for the 10 best models.
^cinterface Root Mean Square Deviation for the 200 models.
^dHADDOCK score was calculated as a weighted sum of intermolecular electrostatic, van der Waals contacts, desolvation, AIR energies and a buried surface area term.
^eIntermolecular energy.
^fBuried surface area.
^gFraction of native contacts.

ISSN: 1471-2105