Docking Predictions of Protein-Protein Interactions and Their Assessment: The CAPRI Experiment - Identification of Ligand Binding Site and Protein-Protein Interaction Area - page 93

Fig. 5.1 A successful docking prediction. Target T37 was submitted for blind prediction during
Round 16 of CAPRI, held in November 2008. The target, a complex of the small GTPase Arf6 with the
LZ2 leucine zipper of the JIP4 effector protein, was a gift of Dr. Julie Ménétrey (Institut Curie, Paris).
Predictors were given an unbound Arf6 structure, and the amino acid sequence of LZ2, which they
had to model build before docking on Arf6. The figure represents the X-ray structure (PDB code
2 W83, Isabet et al. 2009 ) with Arf6 in cyan, LZ2 in pink . The dots are the centers of mass of LZ2
in the models submitted by the 39 predictor groups and the 11 scorer groups who participated in
Round 16. The dots are green for good quality models, blue for “acceptable” models, and yellow
for incorrect models. All the models can be accessed at http://www.ebi.ac.uk/msd-srv/capri/
round16/ (Courtesy of Dr. Marc Lensink (Lille))

were subjected twice for prediction, first with both components unbound, then with
the more flexible component in its bound conformation. The second step always
yielded much better models; for instance, prediction of the protein/RNA complex
failed with the unbound RNA, but there were many good models with the bound
RNA, which has a very different conformation (Lensink and Wodak 2010 ) .

5.5 Flexible Docking and the Scoring Experiment

5.5.1 Simulating Conformation Changes and Mechanisms

of Recognition

Two very important objectives of CAPRI were to stimulate the development of
new methods, and create a forum where they could be discussed and information
would spread within the community. The experiment succeeded on both grounds.