MEGADOCK 4.0: an ultra-high-performance protein-protein docking software for heterogeneous supercomputers

Masahito Ohue; Takehiro Shimoda; Shuji Suzuki; Yuri Matsuzaki; Takashi Ishida; Yutaka Akiyama

doi:10.1093/bioinformatics/btu532

MEGADOCK 4.0: an ultra-high-performance protein-protein docking software for heterogeneous supercomputers

Bioinformatics. 2014 Nov 15;30(22):3281-3. doi: 10.1093/bioinformatics/btu532. Epub 2014 Aug 6.

Authors

Masahito Ohue¹, Takehiro Shimoda¹, Shuji Suzuki², Yuri Matsuzaki³, Takashi Ishida³, Yutaka Akiyama¹

Affiliations

¹ 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.
² 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.
³ 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.

Abstract

Summary: 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.

Availability and implementation: 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.

Contact: akiyama@cs.titech.ac.jp

Supplementary information: Supplementary data are available at Bioinformatics online.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Computers
Molecular Docking Simulation / methods*
Protein Interaction Mapping / methods*
Software*