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  • Title: MEGADOCK 4.0: an ultra-high-performance protein-protein docking software for heterogeneous supercomputers.
    Author: Ohue M, Shimoda T, Suzuki S, Matsuzaki Y, Ishida T, Akiyama Y.
    Journal: Bioinformatics; 2014 Nov 15; 30(22):3281-3. PubMed ID: 25100686.
    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.
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