Prediction of Protein-Protein Binding Interfaces - Identification of Ligand Binding Site and Protein-Protein Interaction Area - page 116

HADDOCK - F-measure - BEST

0.6

0.5

0.4

A
B

0.3

0.2

0.1

0

HADDOCK - F-measure - LOWEST

0.5

0.4

0.3

A
B

0.2

0.1

0

Fig. 6.10 Best ( top ) and worst ( bottom ) solutions produced by HADDOCK and ranked according
to the F-measure criterion. A, B - chain identification

It is worth noting that over 60% of complexes produced by ROSETTA-Dock
achieved a score higher than 0.8 on the MCC scale, while 71% obtained a score
higher than 0.4 on the F-measure scale (Figs. 6.12 and 6.13 ).

6.3.4 ZDOCK

The ZDOCK service deployed at http://zdock.umassmed.edu/ can be used to
perform computations. Input consists of structural descriptions of two protein mol-
ecules. The user should also specify which molecule is to act as a receptor (the
remaining molecule is treated as the ligand and subjected to dynamic docking).
From a computational standpoint, it is advisable to select the smaller molecule as
the ligand. Within the ligand, certain residues can be excluded from the binding site
(this usually involves a handful of residues that are on the opposite side of where the