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

BMC Bioinformatics

Table 2 Data for the 10 best complex models for other test cases, such as YY1, WT1 and Aart, generated with two AIRs in each domain. Standard deviations are shown as subscripts.

Complex names	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
YY1	173/200	1.77_0.26	2.07_0.36	-154.34_2.52	-110.77_35.68	2659.42_58.95	0.76_0.04
WT1	189/200	2.06_0.24	2.14_0.22	-213.34_6.69	-749.97_60.01	2757.10_56.41	0.76_0.04
Aart	200/200	2.74_0.19	2.76_0.21	-222.67_4.04	-819.68_54.57	2896.50_121.53	0.73_0.05

^aNumber of wrap-around models from analysis of 200 complex models.
^binterface Root Mean Square Deviation calculated for the 10 best models.
^cinterface Root Mean Square Deviation calculated 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