論文

• Yuri Matsuzaki, Nobuyuki Uchikoga, Masahito Ohue, Yutaka Akiyama. Rigid-Docking Approaches to Explore Protein–Protein Interaction Space, Advances in Biochemical Engineering/Biotechnology(Network Biology), Springer, Cham, volume 160, pp. 33-35, May 2017.  公式リンク  
  
• Nobuyuki Uchikoga, Yuri Matsuzaki, Masahito Ohue, Yutaka Akiyama. Specificity of broad protein interaction surfaces for proteins with multiple binding partners, Biophysics and Physicobiology, THE BIOPHYSICAL SOCIETY OF JAPAN, Vol. 13, pp. 105-115, July 2016.  公式リンク  
  
• Masahito Ohue, Yuri Matsuzaki, Nobuyuki Uchikoga, Takashi Ishida, Yutaka Akiyama. MEGADOCK: An all-to-all protein-protein interaction prediction system using tertiary structure data, Protein and Peptide Letters, Bentham Science, Volume 21, Issue 8, Page 766-778, June 2014.  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  
  
• Yuri Matsuzaki, Masahito Ohue, Nobuyuki Uchikoga, Yutaka Akiyama. Protein-protein interaction network prediction by using rigid-body docking tools: application to bacterial chemotaxis, Protein and Peptide Letters, Bentham Science, Volume 21, Issue 8, pp. 790-798, July 2013.  公式リンク  
  
• Nobuyuki Uchikoga, Yuri Matsuzaki, Masahito Ohue, Takatsugu Hirokawa, Yutaka Akiyama. Re-docking scheme for generating near-native protein complexes by assembling residue interaction fingerprints, PLOS ONE, Vol. 8, No. 7, e69365, July 2013.  公式リンク  
  

国際会議発表 (査読なし・不明)

• Masahito Ohue, Yuri Matsuzaki, Nobuyuki Uchikoga, Takashi Ishida, Yutaka Akiyama. MEGADOCK 4.0: an ultra-high-performance protein-protein docking software for heterogeneous supercomputers, Biophysical Society 60th Annual Meeting, Feb. 2016.
• Nobuyuki Uchikoga, Yuri Matsuzaki, Masahito Ohue, Yutaka Akiyama. Analysis of Physico-Chemical Properties of Protein Docking Decoys Generated by Rigid-Body Docking, Biophysical Society 60th Annual Meeting, Feb. 2016.
• Nobuyuki Uchikoga, Yuri Matsuzaki, Masahito Ohue, Takatsugu Hirokawa, Yutaka Akiyama. Analysis of protein docking decoys in terms of physicochemical properties of protein surfaces using rigid-body docking process, 3nd IIT Madras – Tokyo Tech Joint Symposium on Algorithms and Applications of Bioinformatics, Nov. 2015.  公式リンク  
  
• Yuri Matsuzaki, Masahito Ohue, Nobuyuki Uchikoga, Takashi Ishida, Yutaka Akiyama. MEGADOCK: A high-performance protein-protein interaction prediction software for petascale supercomputing environments, 3nd IIT Madras – Tokyo Tech Joint Symposium on Algorithms and Applications of Bioinformatics, Nov. 2015.
• Yuri Matsuzaki, Nobuyuki Uchikoga, Masahito Ohue, Yutaka Akiyama. Prediction of human-virus protein-protein interactions by exhaustive rigid docking., Biophysical Society 59th Annual Meeting, Feb. 2015.
• Nobuyuki Uchikoga, Yuri Matsuzaki, Masahito Ohue, Takatsugu Hirokawa, Yutaka Akiyama. Analysis of amino acid properties in interaction surfaces of decoys generated by re-docking, Biophysical Society 59th Annual Meeting, Feb. 2015.
• Nobuyuki Uchikoga, Yuri Matsuzaki, Masahito Ohue, Takatsugu Hirokawa, Yutaka Akiyama. Re-docking scheme to explore docking search space by using interaction profiles, Biophysical Society 58th Annual Meeting, Feb. 2014.
• Yuri Matsuzaki, Nobuyuki Uchikoga, Masahito Ohue, Takashi Ishida, Yutaka Akiyama. Prediction of protein-protein interactions based on tertiary structures and transcription information, Biophysical Society 58th Annual Meeting, Feb. 2014.
• 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.
• Yuri Matsuzaki, Nobuyuki Uchikoga, Masahito Ohue, Takashi Ishida, Yutaka Akiyama. Protein-protein interaction network prediction by using rigid-body docking tool MEGADOCK, Biophysical Society 57th Annual Meeting, Feb. 2013.

国内会議発表 (査読なし・不明)

• 内古閑伸之, 松崎由理, 大上雅史, 秋山泰. 細菌走化性におけるタンパク質間相互作用面の解析, 第16回日本蛋白質科学会年会, June 2016.
• 大上雅史, 内古閑伸之, 松崎由理, 秋山泰. アミノ酸プロファイルによるタンパク質ペプチド複合体のポストドッキング解析, 第53回日本生物物理学会年会, Sept. 2015.
• 内古閑伸之, 松崎由理, 大上雅史, 秋山泰. 剛体アンサンブルドッキングによって得られた候補構造群における相互作用残基ペアの特徴の解析, 第53回日本生物物理学会年会, Sept. 2015.
• 大上雅史, 内古閑伸之, 松崎由理, 秋山泰. タンパク質間相互作用残基の物理化学的性質による単純化プロファイルを用いたポストドッキング解析, 第15回日本蛋白質科学会年会, June 2015.
• 内古閑伸之, 松崎由理, 大上雅史, 広川貴次, 秋山泰. Analysis of properties of protein-protein interaction surface areas involved in more near-native conmplexes by Re-docking scheme, 第52回日本生物物理学会年会, Sept. 2014.
• 大上雅史, 松崎由理, 内古閑伸之, 石田貴士, 秋山泰. MEGADOCK: a high-performance protein-protein interaction prediction tool on supercomputing environments, 第52回日本生物物理学会年会, 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.
• 大上雅史, 松崎由理, 内古閑伸之, 石田貴士, 秋山泰. MEGADOCK：構造ドッキング計算を用いたタンパク質間相互作用の大規模予測, 第13回日本蛋白質科学会年会, 1P-059, June 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.
• 秋山泰, 松崎由理, 石田貴士, 大上雅史, 内古閑 伸之. 網羅的タンパク質ドッキング予測プログラムMEGADOCKの開発と応用, 文部科学省「革新的ハイパフォーマンス・コンピューティング・インフラ （HPCI） の構築」HPCI戦略プログラム「グランドチャレンジ・アプリケーションの研究開発」公開シンポジウム, Mar. 2013.
• 松崎由理, 大上雅史, 石田貴士, 内古閑伸之, 秋山泰. 大規模タンパク質間ネットワーク推定に関する研究, 平成24年度「京」を中核とするHPCIシステム利用研究課題中間報告会, Mar. 2013.

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