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Table 5 Protein-DNA complexes generated for wild-type WRKY DBD with DNA motif using HADDOCK server

From: Molecular dynamics simulations revealed structural differences among WRKY domain-DNA interaction in barley (Hordeum vulgare)

Models

HADDOCK score (a.u)

RMSD (A°)

Van der Waals energy (Kcal/mol)

Electrostatic energy (J)

Desolvation energy (kcal/mol

Restraints violation energy(kcal/mol)

Buried Surface Area (Ã…2)

Z-Score

Cluster 1

−90.5 ± 0.9

14.8 ± 0.2

−35.6 ± 3.8

− 349.8 ± 21.3

11.9 ± 2.3

30.5 ± 29.20

1056.7 ± 63.5

−1.1

Cluster 2

−89.8 ± 4.0

1.3 ± 0.9

−32.7 ± 4.8

− 348.4 ± 23.3

11.1 ± 2.3

14.4 ± 16.81

900.6 ± 115.4

− 1.0

Cluster 3

−77.4 ± 1.7

11.1 ± 0.9

−20.6 ± 3.1

− 361.5 ± 8.7

13.9 ± 2.9

16.6 ± 7.92

753.2 ± 71.2

−0.3

Cluster 4

−53.0 ± 14.4

8.8 ± 0.1

−29.6 ± 7.0

− 192.6 ± 32.9

13.0 ± 4.6

21.6 ± 22.34

971.4 ± 204.7

1.2

Cluster 5

−52.1 ± 13.3

13.8 ± 0.4

−21.9 ± 3.8

− 234.6 ± 62.1

11.4 ± 3.7

53.0 ± 32.58

625.3 ± 135.8

1.2

  1. Bold cluster selected for further analysis