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

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

doi:10.1093/bioinformatics/btu532

Masahito Ohue, Takashi Ishida + Show 4 more

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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

Highlights

Protein–protein interactions can provide valuable insights for understanding the principles of biological systems and for elucidating causes of incurable diseases
Many structures of interacting proteins have been determined by X-ray crystallography and Nuclear Magnetic Resonance (NMR) spectroscopy, the structures of many protein complexes have still not been determined experimentally due to cost and technical limitations
A number of fast Fourier transform (FFT)-based rigid-body initial protein-protein docking tools have been developed for predicting protein complex structures (Cheng et al, 2007; Ritchie and Venkatraman, 2010; Pierce et al, 2011)

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INTRODUCTION

Protein–protein interactions can provide valuable insights for understanding the principles of biological systems and for elucidating causes of incurable diseases. Some applications require a huge number of dockings, such as ensemble docking techniques using multiple conformations for flexible docking (Grünberg et al, 2004; Król et al., 2007), cross-docking for identification of protein interaction partners (Matsuzaki et al, 2009; Wass et al, 2011; Lopes et al, 2013; Zhang et al, 2014), and multiple docking (Karaca and Bonvin, 2011). To achieve these large-scale analyses, use of the supercomputing environment has become absolutely necessary. This implementation guarantees fault tolerance in that the master process surveys all docking jobs

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