Table 2

Ranking of the poses of natural compounds and test set inhibitors (9i and 10i) in the target NF-kappaB p50 both as dimer (p50-p50) and as monomers (p50 A and B). In the docking protocol 1 the similarity scoring algorithm is not used.
Docking protocol 1
 Docking protocol 2
p50-p50
 p50-p50
 p50 (A)
 p50 (B)
Cpd.
 G-score
G-Score
 Cpd.
 G-Score
 Cpd.
 G-Score
10i
 -5.61
 21
 -2.34
 9i
 -3.81
 9i
 -2.13
15
 -5.50
 9i
 -2.29
 10i
 -2.27
 10i
 -1.43
25
 -5.24
 10i
 -2.19
 21
 -1.40
 21
 -0.32
23
 -4.94
 18
 -0.50
 18
 -0.07
 18
 > 0
21
 -4.91
 23
 -0.05
 10
 > 0
 15
 > 0
24
 -4.74
 20
 > 0
 23
 > 0
 23
 > 0
9i
 -4.44
 15
 > 0
 7
 > 0
 24
 > 0
10
 -4.40
 25
 > 0
 8
 > 0
 10
 > 0
20
 -4.37
 24
 > 0
 20
 > 0
 23
 > 0
7
 -4.28
 10
 > 0
 15
 > 0
 20
 > 0
22
 -4.13
 16
 > 0
 25
 > 0
 16
 > 0
16
 -3.48
 7
 > 0
 24
 > 0
 7
 > 0
19
 -3.71
 22
 > 0
 13
 > 0
 8
 > 0
2
 -3.39
 19
 > 0
 12
 > 0
 2
 > 0
27
 -3.09
 4
 > 0
 16
 > 0
 22
 > 0
5
 -3.05
 2
 > 0
 6
 > 0
 4
 > 0
26
 -2.89
 5
 > 0
 9
 > 0
 1
 > 0
18
 -2.69
 27
 > 0
 11
 > 0
 19
 > 0
14
 -2.47
 26
 > 0
 2
 > 0
 14
 > 0
4
 -2.00
 14
 > 0
 3
 > 0
 5
 > 0

Piccagli et al. BMC Structural Biology 2008 8:38   doi:10.1186/1472-6807-8-38