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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.

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

AIR types

Wrap-arounda conformation

RMSDb (Å)

HADDOCK

scorec

Einterd (kcal mol-1)

BSAe

2)

Pairwise

193/200

1.220.47

-200.556.52

-858.3332.43

2165.77102.56

Non-pairwise

167/200

1.260.80

-206.074.54

-846.0142.94

2273.60125.63

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