Docking Predictions of Protein-Protein Interactions and Their Assessment: The CAPRI Experiment - Identification of Ligand Binding Site and Protein-Protein Interaction Area - page 85

Chapter 5
Docking Predictions of Protein-Protein
Interactions and Their Assessment:
The CAPRI Experiment
Joël Janin
Abstract Protein-protein docking was born in the 1970s as a tool to analyze
macromolecular recognition. It developed afterwards into a method of prediction of
the mode of association between proteins of known structure. Since 2001, the perfor-
mance of docking procedures has been assessed in blind predictions by the CAPRI
(Critical Assessment of PRedicted Interactions) experiment. The results show that
docking routinely yields good models of the protein-protein complexes that undergo
only minor changes in conformation and associate as rigid bodies. In contrast, flexible
recognition accompanying large conformation changes in the components remains
difficult to simulate, and structural predictions generally yield lower quality models.
In recent years, a new challenge has been to predict affinity and to estimate the stabil-
ity of the complex along with its structure. Over the years, CAPRI has proved to be
a strong incentive to develop new flexible docking procedures and more discrimina-
tive scoring functions, and it has provided a common ground for discussing methods
and questions related to protein-protein recognition.
Keywords Community-wide experiment • Protein-protein recognition • Binding
af fi nity • Protein fl exibility • Protein engineering • Docking simulation
• Computational biology • DOCK • CAPRI • Rigid body docking • Cube representation
• Geometric hashing algorithm • Monte-Carlo • RosettaDock • Template-based
docking • CASP • Blind prediction • Flexible docking • Molecular dynamics
• Flexibility • Af fi nity benchmark
J. Janin ( * )
IBBMC , Université Paris-Sud , 91405 , Orsay , France
e-mail: [e-mail]