Computational Approaches to Protein-Protein Docking

Protein-protein interactions are known to play significant roles in many biological processes. Knowing the detailed structure of protein-protein complex has become a very important issue in biological sciences. Protein-protein docking methods have been developed for many years in predicting the 3D-structure of protein-protein complexes when the structures of their protein components are available. The protein-protein docking problem involves two key elements: search algorithm and scoring function. The scoring function should be able to recognize the correctly docked complexes from incorrect ones and the search algorithm explores the huge conformational space extensively to find a nearly correct association of the protein components. A docking method becomes successful by combining the two key elements properly and adapting reasonable procedures. In this review, a brief background of protein-protein docking is introduced. Several widely-used docking programs are described and compared. The Critical Assessment of PRedicted Interactions (CAPRI) community-wide experiment, where docking methods have been tested over the past several years, is presented. In conclusion, future directions of protein-protein docking and its applications will be discussed.