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

BMC Bioinformatics

Table 3 Data for the 10 best structures of the Sp1-DNA complex models generated with pairwise and non-pairwise AIR sets. Standard deviations are shown as subscript.

AIR types	Wrap-around^a conformation	RMSD^b (Å)	HADDOCK score^c	E_inter^d (kcal mol^-1)	BSA^e (Å²)
Pairwise	193/200	1.22_0.47	-200.55_6.52	-858.33_32.43	2165.77_102.56
Non-pairwise	167/200	1.26_0.80	-206.07_4.54	-846.01_42.94	2273.60_125.63

^aNumber of wrap-around models from analysis of 200 complex models.
^bRoot Mean Square Deviation calculated for the 10 best models from the lowest energy structure.
^cHADDOCK score was calculated as a weighted sum of intermolecular electrostatic, van der Waals contacts, desolvation, AIR energies and a buried surface area term.
^dIntermolecular energy.
^eBuried surface area.

ISSN: 1471-2105