title: MEGADOCK 4.0: an ultra-high-performance protein-protein docking software for heterogeneous supercomputers.
abstract: CONCLUSIONS
  The application of protein-protein docking in large-scale interactome analysis is a major challenge in structural bioinformatics and requires huge computing resources. In this work, we present MEGADOCK 4.0, an FFT-based docking software that makes extensive use of recent heterogeneous supercomputers and shows powerful, scalable performance of >97% strong scaling.
  
  
  METHODS
  MEGADOCK 4.0 is written in C++ with OpenMPI and NVIDIA CUDA 5.0 (or later) and is freely available to all academic and non-profit users at: http://www.bi.cs.titech.ac.jp/megadock.
  
  
  BACKGROUND
  akiyama@cs.titech.ac.jp
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Department of Computer Science, Graduate School of Information Science and Engineering, Tokyo Institute of Technology, 2-12-1 W8-76, Ookayama, Meguro-ku, Tokyo 152-8550, Japan, Japan Society for the Promotion of Science (JSPS) and Education Academy of Computational Life Sciences (ACLS), Tokyo Institute of Technology, 2-12-1 W8-93, Ookayama, Meguro-ku, Tokyo 152-8550, Japan Department of Computer Science, Graduate School of Information Science and Engineering, Tokyo Institute of Technology, 2-12-1 W8-76, Ookayama, Meguro-ku, Tokyo 152-8550, Japan, Japan Society for the Promotion of Science (JSPS) and Education Academy of Computational Life Sciences (ACLS), Tokyo Institute of Technology, 2-12-1 W8-93, Ookayama, Meguro-ku, Tokyo 152-8550, Japan.
authors.forename: Masahito
authors.initials: M
authors.lastname: Ohue
authors.affiliation: Department of Computer Science, Graduate School of Information Science and Engineering, Tokyo Institute of Technology, 2-12-1 W8-76, Ookayama, Meguro-ku, Tokyo 152-8550, Japan, Japan Society for the Promotion of Science (JSPS) and Education Academy of Computational Life Sciences (ACLS), Tokyo Institute of Technology, 2-12-1 W8-93, Ookayama, Meguro-ku, Tokyo 152-8550, Japan Department of Computer Science, Graduate School of Information Science and Engineering, Tokyo Institute of Technology, 2-12-1 W8-76, Ookayama, Meguro-ku, Tokyo 152-8550, Japan, Japan Society for the Promotion of Science (JSPS) and Education Academy of Computational Life Sciences (ACLS), Tokyo Institute of Technology, 2-12-1 W8-93, Ookayama, Meguro-ku, Tokyo 152-8550, Japan.
authors.forename: Takehiro
authors.initials: T
authors.lastname: Shimoda
authors.affiliation: Department of Computer Science, Graduate School of Information Science and Engineering, Tokyo Institute of Technology, 2-12-1 W8-76, Ookayama, Meguro-ku, Tokyo 152-8550, Japan, Japan Society for the Promotion of Science (JSPS) and Education Academy of Computational Life Sciences (ACLS), Tokyo Institute of Technology, 2-12-1 W8-93, Ookayama, Meguro-ku, Tokyo 152-8550, Japan Department of Computer Science, Graduate School of Information Science and Engineering, Tokyo Institute of Technology, 2-12-1 W8-76, Ookayama, Meguro-ku, Tokyo 152-8550, Japan, Japan Society for the Promotion of Science (JSPS) and Education Academy of Computational Life Sciences (ACLS), Tokyo Institute of Technology, 2-12-1 W8-93, Ookayama, Meguro-ku, Tokyo 152-8550, Japan Department of Computer Science, Graduate School of Information Science and Engineering, Tokyo Institute of Technology, 2-12-1 W8-76, Ookayama, Meguro-ku, Tokyo 152-8550, Japan, Japan Society for the Promotion of Science (JSPS) and Education Academy of Computational Life Sciences (ACLS), Tokyo Institute of Technology, 2-12-1 W8-93, Ookayama, Meguro-ku, Tokyo 152-8550, Japan.
authors.forename: Shuji
authors.initials: S
authors.lastname: Suzuki
authors.affiliation: Department of Computer Science, Graduate School of Information Science and Engineering, Tokyo Institute of Technology, 2-12-1 W8-76, Ookayama, Meguro-ku, Tokyo 152-8550, Japan, Japan Society for the Promotion of Science (JSPS) and Education Academy of Computational Life Sciences (ACLS), Tokyo Institute of Technology, 2-12-1 W8-93, Ookayama, Meguro-ku, Tokyo 152-8550, Japan.
authors.forename: Yuri
authors.initials: Y
authors.lastname: Matsuzaki
authors.affiliation: Department of Computer Science, Graduate School of Information Science and Engineering, Tokyo Institute of Technology, 2-12-1 W8-76, Ookayama, Meguro-ku, Tokyo 152-8550, Japan, Japan Society for the Promotion of Science (JSPS) and Education Academy of Computational Life Sciences (ACLS), Tokyo Institute of Technology, 2-12-1 W8-93, Ookayama, Meguro-ku, Tokyo 152-8550, Japan.
authors.forename: Takashi
authors.initials: T
authors.lastname: Ishida
authors.affiliation: Department of Computer Science, Graduate School of Information Science and Engineering, Tokyo Institute of Technology, 2-12-1 W8-76, Ookayama, Meguro-ku, Tokyo 152-8550, Japan, Japan Society for the Promotion of Science (JSPS) and Education Academy of Computational Life Sciences (ACLS), Tokyo Institute of Technology, 2-12-1 W8-93, Ookayama, Meguro-ku, Tokyo 152-8550, Japan Department of Computer Science, Graduate School of Information Science and Engineering, Tokyo Institute of Technology, 2-12-1 W8-76, Ookayama, Meguro-ku, Tokyo 152-8550, Japan, Japan Society for the Promotion of Science (JSPS) and Education Academy of Computational Life Sciences (ACLS), Tokyo Institute of Technology, 2-12-1 W8-93, Ookayama, Meguro-ku, Tokyo 152-8550, Japan.
authors.forename: Yutaka
authors.initials: Y
authors.lastname: Akiyama
mesh_terms: D003201:Computers; D062105:Molecular Docking Simulation / Q000379:methods*; D025941:Protein Interaction Mapping / Q000379:methods*; D012984:Software
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