Protein-protein interaction (PPI) plays a core role in cellular functions. In recent years, PPI prediction methods based on protein docking have been developed and have been applied for large-scale PPI network prediction based on tertiary structures. We have developed an ultra-high-throughput PPI prediction system based on rigid-body protein-protein docking and supercomputing, named MEGADOCK[1, 2]. MEGADOCK can perform faster docking based on its improved scoring function[3] and implementation for heterogeneous supercomputers[2, 4-6]. MEGADOCK achieved excellent scalability on supercomputing environments, such as K computer and TSUBAME, and realized genome-wide scale PPI network prediction. We applied the MEGADOCK system to a number of interactome analyses; (a) bacterial chemotaxis[7], (b) human apoptosis[8], (c) human EGFR signaling, and (d) RNA decay at the early cellular reprogramming stage[9]. In addition, we have constructed an integrated database of PPI predictions named MEGADOCK-Web[10] to accelerate PPI researches. MEGADOCK-Web provides the four functions, 1) Searching PPI predictions from 28,331,628 prediction results, 2) displaying known PPI, 3) visualizing candidate of interaction with query protein on a biochemical pathway, and 4) visualizing predicted complex structure by a 3D molecular viewer.
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