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- Title
MEGADOCK 4.0: an ultra–high-performance protein–protein docking software for heterogeneous supercomputers.
- Authors
Matsuzaki, Yuri; Ishida, Takashi; Ohue, Masahito; Shimoda, Takehiro; Akiyama, Yutaka; Suzuki, Shuji
- 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.jpSupplementary information: Supplementary data are available at Bioinformatics online
- Subjects
SIGNAL recognition particle receptor; GRAPHICS processing units; BIOINFORMATICS software; SUPERCOMPUTERS; PROTEIN-protein interactions
- Publication
Bioinformatics, 2014, Vol 30, Issue 22, p3281
- ISSN
1367-4803
- Publication type
Article