Prediction of Protein-Protein Binding Interfaces - Identification of Ligand Binding Site and Protein-Protein Interaction Area - page 120

ZDOCK - MCC BEST

1

0.96

0.92

0.88

0.84

0.8

ZDOCK - MCC LOWEST

0.6

0.5

0.4

0.3

0.2
0.1

0

Fig. 6.14 Best ( top ) and worst ( bottom ) results produced by ZDOCK and ranked according to the
MCC criterion. Only chain A is shown

Table 6.2 Comparison of correct and incorrect solutions, indicating the validity of various
models

Lowest →

Best ↓ FOD HADDOCK RosettaDock ZDOCK

FOD 1SD6 1BEB 1G8M

1 T09 1 T09 1 T09

2QM8 1TR8 1YGA

3FYF 2R52

HADDOCK 3SDH / LL 1QLL 1 V94

2QX0 / LL 2BQP 2E4U

2GQR 3D57

RosettaDock 1DVZ / LL
ZDOCK 1X2I
2FJT
2Q3A
3GWL / LL
3GYZ / LL
“LL” stands for “ large ligand ”, which, in the case of the “fuzzy oil drop” model, plays a key role
in shaping the molecule's hydrophobic core, outstripping the influence of complexation events