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

  title={MEGADOCK 4.0: an ultra–high-performance protein–protein docking software for heterogeneous supercomputers},
  author={Masahito Ohue and Takehiro Shimoda and Shuji Suzuki and Yuri Matsuzaki and Takashi Ishida and Yutaka Akiyama},
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… CONTINUE READING
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