title: MEGADOCK 3.0: a high-performance protein-protein interaction prediction software using hybrid parallel computing for petascale supercomputing environments.
abstract: BACKGROUND
  Protein-protein interaction (PPI) plays a core role in cellular functions. Massively parallel supercomputing systems have been actively developed over the past few years, which enable large-scale biological problems to be solved, such as PPI network prediction based on tertiary structures.
  
  
  RESULTS
  We have developed a high throughput and ultra-fast PPI prediction system based on rigid docking, "MEGADOCK", by employing a hybrid parallelization (MPI/OpenMP) technique assuming usages on massively parallel supercomputing systems. MEGADOCK displays significantly faster processing speed in the rigid-body docking process that leads to full utilization of protein tertiary structural data for large-scale and network-level problems in systems biology. Moreover, the system was scalable as shown by measurements carried out on two supercomputing environments. We then conducted prediction of biological PPI networks using the post-docking analysis.
  
  
  CONCLUSIONS
  We present a new protein-protein docking engine aimed at exhaustive docking of mega-order numbers of protein pairs. The system was shown to be scalable by running on thousands of nodes. The software package is available at: http://www.bi.cs.titech.ac.jp/megadock/k/.
authors.affiliation: Graduate School of Information Science and Engineering, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan. y_matsuzaki@bi.cs.titech.ac.jp.
authors.forename: Yuri
authors.initials: Y
authors.lastname: Matsuzaki
authors.forename: Nobuyuki
authors.initials: N
authors.lastname: Uchikoga
authors.forename: Masahito
authors.initials: M
authors.lastname: Ohue
authors.forename: Takehiro
authors.initials: T
authors.lastname: Shimoda
authors.forename: Toshiyuki
authors.initials: T
authors.lastname: Sato
authors.forename: Takashi
authors.initials: T
authors.lastname: Ishida
authors.forename: Yutaka
authors.initials: Y
authors.lastname: Akiyama