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

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

Author information

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.

PMID:
25100686
PMCID:
PMC4221127
DOI:
10.1093/bioinformatics/btu532
[Indexed for MEDLINE]
Free PMC Article
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