Megadock 4.0. An Ultra-High-Performance Protein-Protein Docking Software for Heterogeneous Supercomputers

Abstract

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. However, such network prediction requires much computing resources, and a faster PPI prediction method is eagerly demanded. We have developed an ultra-high-throughput PPI prediction system based on rigid-body protein docking, “MEGADOCK 4.0”. MEGADOCK 4.0 can perform faster docking based on its original scoring function and implementation for heterogeneous supercomputers. MEGADOCK 4.0 was implemented by two parallelization techniques for massively parallel supercomputing environment; the MPI and OpenMP hybrid parallelization and a CUDA-based implementation on GPUs. MEGADOCK 4.0 achieved an excellent scalability on supercomputing environments, such as K computer and TSUBAME 2.5. We also present newly implemented MEGADOCK for many integrated core architecture like Intel Xeon Phi co-processor. In addition, we have already applied MEGADOCK system to a number of interactome analyses such as (a) bacterial chemotaxis pathway consisted of 101 PDB structures and required 10,201 pairs of protein dockings, (b) human apoptosis pathway consisted of 158 PDB structures and required 24,964 pairs of protein dockings, and (c) human epidermal growth factor receptor related pathway consisted of 1,921 PDB structures and required 3,690,241 pairs of protein dockings. We present a new protein-protein docking engine aimed at exhaustive docking of millions of protein pairs. The system was shown to be scalable when running on thousands of nodes and multiple accelerators.