論文

• Takehiro Shimoda, Shuji Suzuki, Masahito Ohue, Takashi Ishida, Yutaka Akiyama.. Protein-Protein Docking on Hardware Accelerators : Comparison of GPU and MIC Architectures, The Thirteenth Asia-Pacific Bioinformatics Conference (APBC2015), BMC Systems Biology, BioMed Central, Vol. 9, No. Suppl 1, Jan. 2015.  公式リンク  
  
• Ohue, M., Shimoda, T., Suzuki, S., Matsuzaki, Y., Ishida, T., Akiyama, Y.. MEGADOCK 4.0: an ultra–high-performance protein–protein docking software for heterogeneous supercomputers, Bioinformatics, Oxford University Press, Vol. 30, No. 22, pp. 3281-3283, Aug. 2014.  公式リンク  
  
• Masahito Ohue, Yuri Matsuzaki, Takehiro Shimoda, Takashi Ishida, Yutaka Akiyama. Highly Precise Protein-Protein Interaction Prediction Based on Consensus Between Template-Based and de Novo Docking Methods, BMC Proceedings, BioMed Central, Volume 7, Supplement 7, S6, Dec. 2013.  公式リンク  
  
• Yuri Matsuzaki, Nobuyuki Uchikoga, Masahito Ohue, Takehiro Shimoda, Toshiyuki Sato, Takashi Ishida, Yutaka Akiyama. MEGADOCK 3.0: A high-performance protein-protein interaction prediction software using hybrid parallel computing for petascale supercomputing environments, Source Code for Biology and Medicine, BioMed Central, Vol. 8, No. 1, Sept. 2013.  公式リンク  
  

国際会議発表 (査読有り)

• Takehiro Shimoda, Takashi Ishida, Shuji Suzuki, Masahito Ohue, Yutaka Akiyama. MEGADOCK-GPU: Acceleration of Protein-Protein Docking Calculation on GPUs, ACM Conference on Bioinformatics, Computational Biology and Biomedicine 2013 (ACM-BCB 2013), 2nd International Workshop on Parallel and Cloud-based Bioinformatics and Biomedicine (ParBio2013), Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine 2013 (ACM-BCB 2013), Association for Computing Machinery, pp. 883-889, Sept. 2013.  公式リンク  
  
• Masahito Ohue, Yuri Matsuzaki, Takehiro Shimoda, Takashi Ishida, Yutaka Akiyama. Highly Precise Protein-Protein Interaction Prediction Based on Consensus Between Template-Based and de Novo Docking Methods, Great Lakes Bioinformatics Conference 2013, Proceedings of Great Lakes Bioinformatics Conference 2013, pp. 100-109, May 2013.

国際会議発表 (査読なし・不明)

• Masahito Ohue, Takehiro Shimoda, Shuji Suzuki, Takashi Ishida, Yutaka Akiyama. A comparative study of GPU and MIC accelerations in fast Fourier transform-based protein-protein docking, 3nd IIT Madras – Tokyo Tech Joint Symposium on Algorithms and Applications of Bioinformatics, Nov. 2015.
• Masahito Ohue, Takehiro Shimoda, Shuji suzuki, Yuri Matsuzaki, Takashi Ishida, Yutaka Akiyama. MEGADOCK 4.0: an ultra–high-performance protein-protein docking software for heterogeneous supercomputers, APBC 2015: The Thirteenth Asia Pacific Bioinformatics Conference, Jan. 2015.
• Masahito Ohue, Takehiro Shimoda, Shuji suzuki, Yuri Matsuzaki, Takashi Ishida, Yutaka Akiyama. MEGADOCK 4.0: an ultra–high-performance protein-protein docking software for heterogeneous supercomputers, GIW/ISCB-Asia 2014, Dec. 2014.
• Takehiro Shimoda, Takashi Ishida, Shuji Suzuki, Masahito Ohue, Yutaka Akiyama. MEGADOCK-GPU: Acceleration of Protein-Protein Docking Calculation on GPUs, 2nd IIT Madras – Tokyo Tech Joint Symposium on Techniques and Applications of Bioinformatics, P13, Sept. 2013.
• Masahito Ohue, Yuri Matsuzaki, Takehiro Shimoda, Takashi Ishida, Yutaka Akiyama. Highly precise protein-protein interaction prediction by integrating template-based and template-free protein docking, 2nd IIT Madras – Tokyo Tech Joint Symposium on Techniques and Applications of Bioinformatics, P08, Sept. 2013.
• Masahito Ohue, Yuri Matsuzaki, Takehiro Shimoda, Takashi Ishida, Yutaka Akiyama. Improvement of protein-protein interaction prediction by integrating template-based and template-free protein docking, ACM Conference on Bioinformatics, Computatioal Biology and Biomedical Informatics (ACM-BCB2013), p. 667, Sept. 2013.
• Takehiro Shimoda, Masahito Ohue, Yuri Matsuzaki, Takayuki Fujiwara, Nobuyuki Uchikoga, Takashi Ishida, Yutaka Akiyama. The MEGADOCK project: Ultra-high-performance protein-protein interaction prediction tools on supercomputing environments, ACM Conference on Bioinformatics, Computatioal Biology and Biomedical Informatics (ACM-BCB2013), p. 668, Sept. 2013.
• Masahito Ohue, Yuri Matsuzaki, Nobuyuki Uchikoga, Kohei Yamamoto, Takayuki Fujiwara, Takehiro Shimoda, Toshiyuki Sato, Takashi Ishida, Yutaka Akiyama. Protein-protein interaction prediction based on rigid-body docking with ultra-high-performance computing technique: applications to affinity prediction on CAPRI round 21 and interactome analyses, CAPRI 2013 5th Evaluation Meeting, Apr. 2013.

国内会議発表 (査読なし・不明)

• Masahito Ohue, Takehiro Shimoda, Shuji Suzuki, Yuri Matsuzaki, Takashi Ishida, Yutaka Akiyama. MEGADOCK 4.0: an ultra-high-performance protein-protein docking software for heterogeneous supercomputers, IIBMP2014, Bioinformatics, Volume 30, Issue 22, page 3281-3283, Nov. 2014.  公式リンク  
  
• Masahito Ohue, Takehiro Shimoda, Shuji Suzuki, Yuri Matsuzaki, Takashi Ishida, Yutaka Akiyama. The MEGADOCK Project: high-performance protein-protein interaction prediction tools on supercomputing environments, The Asia hub for e-drug discovery symposium 2014 (AHeDD' 2014), Nov. 2014.
• Masahito Ohue, Takehiro Shimoda, Shuji Suzuki, Yuri Matsuzaki, Takashi Ishida, Yutaka Akiyama. The MEGADOCK Project: high-performance protein-protein interaction prediction tools on supercomputing environments, Biophysical Society Thematic Meeting Modeling of Biomolecular Systems Interactions, Dynamics, and Allostery: Bridging Experiments and Computations, Sept. 2014.
• 大上雅史, 下田雄大, 松崎由理, 内古閑伸之, 鈴木脩司, 石田貴士, 秋山泰. MEGADOCK 4.0: mega-dock per dayへの道のり, 生命情報科学若手の会 第5回研究会, Feb. 2014.
• Masahito Ohue, Yuri Matsuzaki, Takehiro Shimoda, Takashi Ishida, Yutaka Akiyama. Highly precise protein-protein interaction prediction by integrating template-based and template-free protein docking, The 2013 Annual Conference of the Japanese Society for Bioinformatics (JSBi2013), P077, Nov. 2013.
• 下田雄大, 石田貴士, 鈴木脩司, 大上雅史, 秋山泰. MEGADOCK-GPU: GPUによるタンパク質間ドッキング計算の高速化, GTC Workshop Japan 2013, No. 1, July 2013.
• 大上雅史, 松崎由理, 内古閑伸之, 山本航平, 下田雄大, 藤原隆之, 石田貴士, 秋山泰. MEGADOCK 3.0：超並列タンパク質間相互作用予測システム, 生命情報科学若手の会 第4回研究会, Mar. 2013.
• 下田雄大, 石田貴士, 秋山泰. タンパク質間ドッキング予測における実空間での効率的な評価スコア計算方法の研究, 情報処理学会研究報告, 第29回バイオ情報学研究会, vol. 2012-BIO-29, no. 20, p. 1-3, June 2012.

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