Prediction of Protein-Protein Binding Interfaces - Identification of Ligand Binding Site and Protein-Protein Interaction Area - page 113

-

Δ H profile and contact map

Protein contact identification ROC curves

1.0

Protein

-

0.006

Δ H ≥ 0.0

-

Δ H ≤ 0.0

0.8

0.004

0.6

0.002

0.0

0.4

-0.002

0.2

-0.004

0.0

50 100 150 200 250 300

0 0.0 0.6

False Positive Rate

0.8 1.0

0.2 0.4

Residue

Δ H profile of the 1YGA homodimer, indicating residues involved in complexation
( left ). The graph on the right-hand side shows the ROC curve corresponding to profile minima
(excess hydrophobicity) and indicates the relation between TPR and FPR for this homodimer

Fig. 6.5

Fig. 6.6 The 1YGA homodimer. White spheres in the A chain indicate residues which correspond
to local

Δ H profile minima (excess hydrophobicity), such as Val and Cys. The presence of such
residues on the molecule surface enables the model to accurately identify complexation sites

6.3.2 HADDOCK

HADDOCK computations were performed using the web service available at http://
haddock.science.uu.nl/enmr/services/HADDOCK/haddockserver-easy.html . Input
data consisted of PDB files describing “active” amino acids. The Gramm-X prepro-
cessing package (Tovchigrechko and Vakser 2006 ) was not used. HADDOCK
works by optimizing binding energy values in a six-dimensional space (three transla-
tions + three rotations). The “passive amino acid” option was skipped.