@article{CTT100839067,
  author = {Guillaume Launay and Masahito Ohue and Julia Prieto Santero and Yuri Matsuzaki and Cécile Hilpert and Nobuyuki Uchikoga and Takanori Hayashi and Juliette Martin},
  title = {Evaluation of CONSRANK-like scoring functions for rescoring ensembles of protein-protein docking poses},
  journal = {Frontiers in Molecular Biosciences},
  year = 2020,
}

@article{CTT100839089,
  author = {Kento Aoyama and Masanori Kakuta and Yuri Matsuzaki and Takashi Ishida and Masahito Ohue and Yutaka Akiyama},
  title = {Development of computational pipeline software for genome/exome analysis on the K computer},
  journal = {Supercomputing Frontiers and Innovations},
  year = 2020,
}

@article{CTT100766873,
  author = {Hayashi T and Matsuzaki Y and Yanagisawa K and Ohue M and Akiyama Y.},
  title = {MEGADOCK-Web: an integrated database of high-throughput structure-based protein-protein interaction predictions},
  journal = {BMC Bioinformatics (In Proc. APBC2018)},
  year = 2018,
}

@article{CTT100766869,
  author = {Yuri Matsuzaki and Nobuyuki Uchikoga and Masahito Ohue and Yutaka Akiyama},
  title = {Rigid-Docking Approaches to Explore Protein–Protein Interaction Space},
  journal = {Advances in Biochemical Engineering/Biotechnology(Network Biology)},
  year = 2017,
}

@article{CTT100715183,
  author = {Nobuyuki Uchikoga and Yuri Matsuzaki and Masahito Ohue and Yutaka Akiyama},
  title = {Specificity of broad protein interaction surfaces for proteins with multiple binding partners},
  journal = {Biophysics and Physicobiology},
  year = 2016,
}

@article{CTT100738049,
  author = {青山 健人 and 角田 将典 and 松崎 由理 and 石田 貴士 and 秋山 泰},
  title = {スーパーコンピュータ「京」上でのエクソーム解析パイプラインの開発},
  journal = {情報処理学会論文誌コンピューティングシステム（ACS）},
  year = 2016,
}

@article{CTT100684742,
  author = {Ohue, M. and Shimoda, T. and Suzuki, S. and Matsuzaki, Y. and Ishida, T. and Akiyama, Y.},
  title = {MEGADOCK 4.0: an ultra–high-performance protein–protein docking software for heterogeneous supercomputers},
  journal = {Bioinformatics},
  year = 2014,
}

@article{CTT100666828,
  author = {Masahito Ohue and Yuri Matsuzaki and Nobuyuki Uchikoga and Takashi Ishida and Yutaka Akiyama},
  title = {MEGADOCK: An all-to-all protein-protein interaction prediction system using tertiary structure data},
  journal = {Protein and Peptide Letters},
  year = 2014,
}

@article{CTT100666826,
  author = {Masahito Ohue and Yuri Matsuzaki and Takehiro Shimoda and Takashi Ishida and Yutaka Akiyama},
  title = {Highly Precise Protein-Protein Interaction Prediction Based on Consensus Between Template-Based and de Novo Docking Methods},
  journal = {BMC Proceedings},
  year = 2013,
}

@article{CTT100666827,
  author = {Yuri Matsuzaki and Nobuyuki Uchikoga and Masahito Ohue and Takehiro Shimoda and Toshiyuki Sato and Takashi Ishida and Yutaka Akiyama},
  title = {MEGADOCK 3.0: A high-performance protein-protein interaction prediction software using hybrid parallel computing for petascale supercomputing environments},
  journal = {Source Code for Biology and Medicine},
  year = 2013,
}

@article{CTT100666831,
  author = {Nobuyuki Uchikoga and Yuri Matsuzaki and Masahito Ohue and Takatsugu Hirokawa and Yutaka Akiyama},
  title = {Re-docking scheme for generating near-native protein complexes by assembling residue interaction fingerprints},
  journal = {PLOS ONE},
  year = 2013,
}

@article{CTT100666829,
  author = {Yuri Matsuzaki and Masahito Ohue and Nobuyuki Uchikoga and Yutaka Akiyama},
  title = {Protein-protein interaction network prediction by using rigid-body docking tools: application to bacterial chemotaxis},
  journal = {Protein and Peptide Letters},
  year = 2013,
}

@article{CTT100631867,
  author = {Sarel J. Fleishman and Timothy A. Whitehead and Eva-Maria Strauch and Jacob E. Corn and Sanbo Qin and Huan-Xiang Zhou and Julie C. Mitchell and Omar N. A. Demerdash and Mayuko Takeda-Shitaka and Genki Terashi and Iain H. Moal and Xiaofan Li and Paul A. Bates and Martin Zacharias and Hahnbeom Park and Jun-su Ko and Hasup Lee and Chaok Seok and Thomas Bourquard and Julie Bernauer and Anne Poupon and Jerome Aze and Seren Soner and Sefik Kerem Oval. and Pemra Ozbek and Nir Ben Tal and Turkan Haliloglu and Howook Hwang and Thom Vreven and Brian G. Pierce and Zhiping Weng and Laura Perez-Cano and Carles Pons and Juan Fernandez-Recio and Fan Jiang and Feng Yang and Xinqi Gong and Libin Cao and Xianjin Xu and Bin Liu and Panwen Wang and Chunhua Li and Cunxin Wang and Charles H. Robert and Mainak Guharoy and Shiyong Liu and Yangyu Huang and Lin Li and Dachuan Guo and Ying Chen and Yi Xiao and Nir London and Zohar Itzhaki and Ora Schueler-Furman and Yuval Inbar and Vladimir Patapov and Mati Cohen and Gideon Schreiber and Yuko Tsuchiya and Eiji Kanamori and Daron M. Standley and Haruki Nakamura and Kengo Kinoshita and Camden M. Driggers and Robert G. Hall and Jessica L. Morgan and Victor L. Hsu and Jian Zhan and Yuedong Yang and Yaoqi Zhou and Panagiotis L. Kastritis and Alexandre M. J. J. Bonvin and Weiyi Zhang and Carlos J. Camacho and Krishna P. Kilambi and Aroop Sircar and Jeffrey J. Gray and Masahito Ohue and Nobuyuki Uchikoga and Yuri Matsuzaki and Takashi Ishida and Yutaka Akiyama and Raed Khashan and Stephen Bush and Denis Fouches and Alexander Tropsha and Juan Esquivel-Rodriguez and Daisuke Kihara and P. Benjamin Stranges and Ron Jacak and Brian Kuhlman and Sheng-You Huang and Xiaoqin Zou and Shoshana J. Wodak and Joel Janin and David Baker},
  title = {Community-Wide Assessment of Protein-Interface Modeling Suggests Improvements to Design Methodology},
  journal = {Journal of Molecular Biology},
  year = 2011,
}

@article{CTT100631869,
  author = {Masahito Ohue and Yuri Matsuzaki and Yutaka Akiyama},
  title = {Docking-calculation-based Method for Predicting Protein-RNA Interactions},
  journal = {Genome Informatics},
  year = 2011,
}

@article{CTT100596607,
  author = {Yuri Matsuzaki and Yusuke Matsuzaki and Toshiyuki Sato and Yutaka Akiyama},
  title = {In silico screening of protein-protein interactions with all-to-all rigid docking and clustering: an application to pathway analysis},
  journal = {Journal of Bioinformatics and Computational Biology},
  year = 2009,
}

@inproceedings{CTT100809992,
  author = {Masahito Ohue and Takanori Hayashi and Yuri Matsuzaki and Keisuke Yanagisawa and Yutaka Akiyama},
  title = {Megadock-Web: An Integrated Database of High-Throughput Structure-Based Protein-Protein Interaction Predictions},
  booktitle = {},
  year = 2019,
}

@inproceedings{CTT100809994,
  author = {Nobuyuki Uchikoga and Yuri Matsuzaki},
  title = {Analysis of amino acid sequences of protein interaction surfaces by rigid-body docking for known and unknown protein complex pairs.},
  booktitle = {},
  year = 2018,
}

@inproceedings{CTT100809993,
  author = {Masahito Ohue and Takanori Hayashi and Hiroki Watanabe and Yuri Matsuzaki and Nobuyuki Uchikoga and Yutaka Akiyama},
  title = {Supercomputing-based exhaustive protein-protein interaction prediction and its open database.},
  booktitle = {},
  year = 2018,
}

@inproceedings{CTT100766884,
  author = {林孝紀 and 山本悠生 and 松崎由理 and 大上雅史 and 秋山泰},
  title = {タンパク質間相互作用予測統合データベースMEGADOCK-WEBの改良とクラウド計算環境との連携},
  booktitle = {研究報告バイオ情報学（BIO）},
  year = 2017,
}

@inproceedings{CTT100806075,
  author = {Yuri Matsuzaki and Simm, Jaak and Uchikoga, Nobuyuki and Yutaka Akiyama},
  title = {A Docking Based Approach to Analyze Interaction Surfaces of Virus-Host Protein-Protein Interactions},
  booktitle = {BIOPHYSICAL JOURNAL},
  year = 2017,
}

@inproceedings{CTT100806049,
  author = {Masahito Ohue and Yamamoto, Yuki and Hayashi, Takanori and Yuri Matsuzaki and Yutaka Akiyama},
  title = {Cloud Computing for All-To-All Protein-Protein Docking on Azure HPC},
  booktitle = {BIOPHYSICAL JOURNAL},
  year = 2017,
}

@inproceedings{CTT100805974,
  author = {Uchikoga, Nobuyuki and Yuri Matsuzaki and Masahito Ohue and Yutaka Akiyama},
  title = {Interaction Surfaces of Proteins Involved in Bacterial Chemotaxis with Rigid-Body Docking Decoys},
  booktitle = {BIOPHYSICAL JOURNAL},
  year = 2017,
}

@inproceedings{CTT100715195,
  author = {Takanori Hayashi and Kazuki Nagasawa and Yuri Matsuzaki and Masahito Ohue and Yutaka Akiyama},
  title = {MEGADOCK-WEB: a database of predicted protein-protein interactions and its web interface},
  booktitle = {},
  year = 2016,
}

@inproceedings{CTT100715161,
  author = {内古閑伸之 and 松崎由理 and 大上雅史 and 秋山泰},
  title = {細菌走化性におけるタンパク質間相互作用面の解析},
  booktitle = {},
  year = 2016,
}

@inproceedings{CTT100701949,
  author = {長澤一輝 and 松崎由理 and 大上雅史 and 秋山泰},
  title = {タンパク質間相互作用予測結果データベース及び表示系の構築},
  booktitle = {研究報告バイオ情報学（BIO）},
  year = 2016,
}

@inproceedings{CTT100715115,
  author = {Nobuyuki Uchikoga and Yuri Matsuzaki and Masahito Ohue and Yutaka Akiyama},
  title = {Analysis of Physico-Chemical Properties of Protein Docking Decoys Generated by Rigid-Body Docking},
  booktitle = {},
  year = 2016,
}

@inproceedings{CTT100806095,
  author = {Yuri Matsuzaki and Simm, Jaak},
  title = {Rigid Docking Based Protein-Protein Interaction Prediction using High Scoring Docking Models},
  booktitle = {BIOPHYSICAL JOURNAL},
  year = 2016,
}

@inproceedings{CTT100715113,
  author = {Masahito Ohue and Yuri Matsuzaki and Nobuyuki Uchikoga and Takashi Ishida and Yutaka Akiyama},
  title = {MEGADOCK 4.0: an ultra-high-performance protein-protein docking software for heterogeneous supercomputers},
  booktitle = {},
  year = 2016,
}

@inproceedings{CTT100715163,
  author = {大上雅史 and 松崎由理 and 石田貴士 and 秋山泰},
  title = {タンパク質間相互作用予測システムMEGADOCKによるEGFRパスウェイ解析},
  booktitle = {},
  year = 2015,
}

@inproceedings{CTT100715131,
  author = {Nobuyuki Uchikoga and Yuri Matsuzaki and Masahito Ohue and Takatsugu Hirokawa and Yutaka Akiyama},
  title = {Analysis of protein docking decoys in terms of physicochemical properties of protein surfaces using rigid-body docking process},
  booktitle = {},
  year = 2015,
}

@inproceedings{CTT100715133,
  author = {Yuri Matsuzaki and Masahito Ohue and Nobuyuki Uchikoga and Takashi Ishida and Yutaka Akiyama},
  title = {MEGADOCK: A high-performance protein-protein interaction prediction software for petascale supercomputing environments},
  booktitle = {},
  year = 2015,
}

@inproceedings{CTT100806093,
  author = {Uchikoga, Nobuyuki and Masahito Ohue and Yuri Matsuzaki and Yutaka Akiyama},
  title = {Post-docking analysis by physicochemical properties of protein-protein interactions generated from rigid-body docking processes},
  booktitle = {PROTEIN SCIENCE},
  year = 2015,
}

@inproceedings{CTT100715170,
  author = {内古閑伸之 and 松崎由理 and 大上雅史 and 秋山泰},
  title = {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},
  booktitle = {},
  year = 2015,
}

@inproceedings{CTT100715168,
  author = {大上雅史 and 内古閑伸之 and 松崎由理 and 秋山泰},
  title = {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},
  booktitle = {},
  year = 2015,
}

@inproceedings{CTT100715173,
  author = {大上雅史 and 内古閑伸之 and 松崎由理 and 秋山泰},
  title = {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},
  booktitle = {},
  year = 2015,
}

@inproceedings{CTT100715140,
  author = {Yuri Matsuzaki and Nobuyuki Uchikoga and Masahito Ohue and Yutaka Akiyama},
  title = {Prediction of human-virus protein-protein interactions by exhaustive rigid docking.},
  booktitle = {},
  year = 2015,
}

@inproceedings{CTT100715136,
  author = {Nobuyuki Uchikoga and Yuri Matsuzaki and Masahito Ohue and Takatsugu Hirokawa and Yutaka Akiyama},
  title = {Analysis of amino acid properties in interaction surfaces of decoys generated by re-docking},
  booktitle = {},
  year = 2015,
}

@inproceedings{CTT100715151,
  author = {Masahito Ohue and Takehiro Shimoda and Shuji suzuki and Yuri Matsuzaki and Takashi Ishida and Yutaka Akiyama},
  title = {MEGADOCK 4.0: an ultra–high-performance protein-protein docking software for heterogeneous supercomputers},
  booktitle = {},
  year = 2015,
}

@inproceedings{CTT100715153,
  author = {Masahito Ohue and Takehiro Shimoda and Shuji suzuki and Yuri Matsuzaki and Takashi Ishida and Yutaka Akiyama},
  title = {MEGADOCK 4.0: an ultra–high-performance protein-protein docking software for heterogeneous supercomputers},
  booktitle = {},
  year = 2014,
}

@inproceedings{CTT100715154,
  author = {Masahito Ohue and Takehiro Shimoda and Shuji Suzuki and Yuri Matsuzaki and Takashi Ishida and Yutaka Akiyama},
  title = {The MEGADOCK Project: high-performance protein-protein interaction prediction tools on supercomputing environments},
  booktitle = {},
  year = 2014,
}

@inproceedings{CTT100715175,
  author = {Masahito Ohue and Takehiro Shimoda and Shuji Suzuki and Yuri Matsuzaki and Takashi Ishida and Yutaka Akiyama},
  title = {MEGADOCK 4.0: an ultra-high-performance protein-protein docking software for heterogeneous supercomputers},
  booktitle = {Bioinformatics},
  year = 2014,
}

@inproceedings{CTT100715174,
  author = {大上雅史 and 松崎由理 and 石田貴士 and 秋山泰},
  title = {タンパク質とペプチドのドッキング計算},
  booktitle = {},
  year = 2014,
}

@inproceedings{CTT100715177,
  author = {内古閑伸之 and 松崎由理 and 大上雅史 and 広川貴次 and 秋山泰},
  title = {Analysis of properties of protein-protein interaction surface areas involved in more near-native conmplexes by Re-docking scheme},
  booktitle = {},
  year = 2014,
}

@inproceedings{CTT100715157,
  author = {Masahito Ohue and Takehiro Shimoda and Shuji Suzuki and Yuri Matsuzaki and Takashi Ishida and Yutaka Akiyama},
  title = {The MEGADOCK Project: high-performance protein-protein interaction prediction tools on supercomputing environments},
  booktitle = {},
  year = 2014,
}

@inproceedings{CTT100715176,
  author = {大上雅史 and 松崎由理 and 内古閑伸之 and 石田貴士 and 秋山泰},
  title = {MEGADOCK: a high-performance protein-protein interaction prediction tool on supercomputing environments},
  booktitle = {},
  year = 2014,
}

@inproceedings{CTT100805086,
  author = {大上 雅史 and 下田 雄大 and 松崎由理 and 石田 貴士 and 秋山泰},
  title = {大規模GPUクラスタによるタンパク質ドッキング計算システム},
  booktitle = {研究報告数理モデル化と問題解決（MPS）},
  year = 2014,
}

@inproceedings{CTT100805483,
  author = {大上 雅史 and 下田 雄大 and 松崎由理 and 石田 貴士 and 秋山泰},
  title = {大規模GPUクラスタによるタンパク質ドッキング計算システム (情報論的学習理論と機械学習)},
  booktitle = {電子情報通信学会技術研究報告 = IEICE technical report : 信学技報},
  year = 2014,
}

@inproceedings{CTT100715219,
  author = {青山 健人 and 角田 将典 and 松崎 由理 and 石田 貴士 and 秋山 泰},
  title = {エクソーム解析パイプラインの京コンピュータ上での大規模並列化},
  booktitle = {情報処理学会研究報告},
  year = 2014,
}

@inproceedings{CTT100801935,
  author = {大上 雅史 and 下田 雄大 and 松崎由理 and 石田貴士 and 秋山泰},
  title = {大規模GPUクラスタによるタンパク質ドッキング計算システム (ニューロコンピューティング)},
  booktitle = {電子情報通信学会技術研究報告 = IEICE technical report : 信学技報},
  year = 2014,
}

@inproceedings{CTT100801959,
  author = {大上雅史 and 下田 雄大 and 松崎由理 and 石田貴士 and 秋山泰},
  title = {大規模GPUクラスタによるタンパク質ドッキング計算システム},
  booktitle = {研究報告バイオ情報学（BIO）},
  year = 2014,
}

@inproceedings{CTT100666854,
  author = {大上雅史 and 下田雄大 and 松崎由理 and 内古閑伸之 and 鈴木脩司 and 石田貴士 and 秋山泰},
  title = {MEGADOCK 4.0: mega-dock per dayへの道のり},
  booktitle = {生命情報科学若手の会 第5回研究会},
  year = 2014,
}

@inproceedings{CTT100666899,
  author = {Yuri Matsuzaki and Nobuyuki Uchikoga and Masahito Ohue and Takashi Ishida and Yutaka Akiyama},
  title = {Prediction of protein-protein interactions based on tertiary structures and transcription information},
  booktitle = {},
  year = 2014,
}

@inproceedings{CTT100666898,
  author = {Nobuyuki Uchikoga and Yuri Matsuzaki and Masahito Ohue and Takatsugu Hirokawa and Yutaka Akiyama},
  title = {Re-docking scheme to explore docking search space by using interaction profiles},
  booktitle = {},
  year = 2014,
}

@inproceedings{CTT100666834,
  author = {Masahito Ohue and Yuri Matsuzaki and Takehiro Shimoda and Takashi Ishida and Yutaka Akiyama},
  title = {Highly precise protein-protein interaction prediction by integrating template-based and template-free protein docking},
  booktitle = {},
  year = 2013,
}

@inproceedings{CTT100666836,
  author = {Masahito Ohue and Yuri Matsuzaki and Takehiro Shimoda and Takashi Ishida and Yutaka Akiyama},
  title = {Highly precise protein-protein interaction prediction by integrating template-based and template-free protein docking},
  booktitle = {},
  year = 2013,
}

@inproceedings{CTT100876463,
  author = {Nobuyuki Uchikoga and Yuri Matsuzaki and Masahito Ohue and Takatsugu Hirokawa and Yutaka Akiyama},
  title = {Re-docking scheme of protein-protein interactions for generating near-native interaction patterns in difficult docking cases},
  booktitle = {},
  year = 2013,
}

@inproceedings{CTT100666838,
  author = {Takehiro Shimoda and Masahito Ohue and Yuri Matsuzaki and Takayuki Fujiwara and Nobuyuki Uchikoga and Takashi Ishida and Yutaka Akiyama},
  title = {The MEGADOCK project: Ultra-high-performance protein-protein interaction prediction tools on supercomputing environments},
  booktitle = {},
  year = 2013,
}

@inproceedings{CTT100666837,
  author = {Masahito Ohue and Yuri Matsuzaki and Takehiro Shimoda and Takashi Ishida and Yutaka Akiyama},
  title = {Improvement of protein-protein interaction prediction by integrating template-based and template-free protein docking},
  booktitle = {},
  year = 2013,
}

@inproceedings{CTT100876464,
  author = {Yuri Matsuzaki and Masahito Ohue and Nobuyuki Uchikoga and Takashi Ishida and Yutaka Akiyama},
  title = {Structure based protein-protein interaction network prediction of EGFR signaling related proteins using MEGADOCK},
  booktitle = {},
  year = 2013,
}

@inproceedings{CTT100666851,
  author = {大上雅史 and 松崎由理 and 内古閑伸之 and 石田貴士 and 秋山泰},
  title = {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},
  booktitle = {第13回日本蛋白質科学会年会},
  year = 2013,
}

@inproceedings{CTT100666833,
  author = {Masahito Ohue and Yuri Matsuzaki and Takehiro Shimoda and Takashi Ishida and Yutaka Akiyama},
  title = {Highly Precise Protein-Protein Interaction Prediction Based on Consensus Between Template-Based and de Novo Docking Methods},
  booktitle = {Proceedings of Great Lakes Bioinformatics Conference 2013},
  year = 2013,
}

@inproceedings{CTT100666845,
  author = {Masahito Ohue and Yuri Matsuzaki and Nobuyuki Uchikoga and Kohei Yamamoto and Takayuki Fujiwara and Takehiro Shimoda and Toshiyuki Sato and Takashi Ishida and Yutaka Akiyama},
  title = {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},
  booktitle = {CAPRI 2013 5th Evaluation Meeting},
  year = 2013,
}

@inproceedings{CTT100666852,
  author = {大上雅史 and 松崎由理 and 内古閑伸之 and 山本航平 and 下田雄大 and 藤原隆之 and 石田貴士 and 秋山泰},
  title = {MEGADOCK 3.0：超並列タンパク質間相互作用予測システム},
  booktitle = {生命情報科学若手の会 第4回研究会},
  year = 2013,
}

@inproceedings{CTT100658033,
  author = {秋山泰 and 松崎由理 and 石田貴士 and 大上雅史 and 内古閑 伸之},
  title = {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},
  booktitle = {},
  year = 2013,
}

@inproceedings{CTT100658089,
  author = {松崎由理 and 大上雅史 and 石田貴士 and 内古閑伸之 and 秋山泰},
  title = {大規模タンパク質間ネットワーク推定に関する研究},
  booktitle = {},
  year = 2013,
}

@inproceedings{CTT100658081,
  author = {Yuri Matsuzaki and Nobuyuki Uchikoga and Masahito Ohue and Takashi Ishida and Yutaka Akiyama},
  title = {Protein-protein interaction network prediction by using rigid-body docking tool MEGADOCK},
  booktitle = {},
  year = 2013,
}

@inproceedings{CTT100658028,
  author = {大上雅史 and 松崎由理 and 石田貴士 and 秋山泰},
  title = {MEGADOCK: 大規模タンパク質間相互作用予測システムとその応用},
  booktitle = {},
  year = 2013,
}

@inproceedings{CTT100658027,
  author = {秋山泰 and 松崎由理 and 大上雅史 and 石田貴士 and 内古閑伸之},
  title = {網羅的タンパク質ドッキング解析プログラムMEGADOCKの開発と応用},
  booktitle = {},
  year = 2013,
}

@inproceedings{CTT100658030,
  author = {Yuri Matsuzaki and Masahito Ohue and Nobuyuki Uchikoga and Takashi Ishida and Yutaka Akiyama},
  title = {Application of exhaustive protein-protein interaction prediction system by using protein docking to signal transduction pathways.},
  booktitle = {},
  year = 2012,
}

@inproceedings{CTT100658031,
  author = {Masahito Ohue and Yuri Matsuzaki and Nobuyuki Uchikoga and Takashi Ishida and Yutaka Akiyama},
  title = {MEGADOCK: A rapid screening system of protein-protein interactions with all-to-all physical docking.},
  booktitle = {},
  year = 2012,
}

@inproceedings{CTT100658083,
  author = {大上雅史 and 松崎由理 and 石田貴士 and 秋山泰},
  title = {MEGADOCKを用いたタンパク質間相互作用予測のヒトアポトーシスパスウェイ解析への応用},
  booktitle = {研究報告バイオ情報学（BIO）},
  year = 2012,
}

@inproceedings{CTT100657808,
  author = {Masahito Ohue and Yuri Matsuzaki and Takashi Ishida and Yutaka Akiyama},
  title = {Improvement of the protein-protein docking prediction by introducing a simple hydrophobic interaction model: an application to interaction pathway analysis.},
  booktitle = {Lecture Notes in Bioinformatics},
  year = 2012,
}

@inproceedings{CTT100658026,
  author = {Yuri Matsuzaki and Masahito Ohue and Nobuyuki Uchikoga and Takashi Ishida and Yutaka Akiyama},
  title = {Application of exhaustive protein-protein interaction prediction system by using protein docking to signal transduction pathways.},
  booktitle = {},
  year = 2012,
}

@inproceedings{CTT100657810,
  author = {Masahito Ohue and Yuri Matsuzaki and Nobuyuki Uchikoga and Takashi Ishida and Yutaka Akiyama},
  title = {MEGADOCK: A rapid screening system of protein-protein interactions with all-to-all physical docking.},
  booktitle = {},
  year = 2012,
}

@inproceedings{CTT100657809,
  author = {Yuri Matsuzaki and Masahito Ohue and Nobuyuki Uchikoga and Takashi Ishida and Yutaka Akiyama},
  title = {Application of exhaustive protein-protein interaction prediction system by using protein docking to signal transduction pathways.},
  booktitle = {},
  year = 2012,
}

@inproceedings{CTT100658029,
  author = {Masahito Ohue and Yuri Matsuzaki and Nobuyuki Uchikoga and Takashi Ishida and Yutaka Akiyama},
  title = {MEGADOCK: A rapid screening system of protein-protein interactions with all-to-all physical docking.},
  booktitle = {},
  year = 2012,
}

@inproceedings{CTT100802108,
  author = {藤原 隆之 and 松崎由理 and 石田貴士 and 秋山泰},
  title = {タンパク質間ドッキング予測における目的関数の機械学習を用いた動的調整},
  booktitle = {電子情報通信学会技術研究報告. NC, ニューロコンピューティング},
  year = 2012,
}

@inproceedings{CTT100658082,
  author = {藤原隆之 and 松崎由理 and 石田貴士 and 秋山泰},
  title = {タンパク質間ドッキング予測における機械学習を用いた目的関数の動的調整},
  booktitle = {情報処理学会研究報告},
  year = 2012,
}

@inproceedings{CTT100634030,
  author = {松崎 由理 and 内古閑 伸之 and 大上 雅史 and 秋山 泰},
  title = {網羅的タンパク質ドッキング解析プログラムMEGADOCKの開発と応用},
  booktitle = {},
  year = 2012,
}

@inproceedings{CTT100633782,
  author = {Masahito Ohue and Yuri Matsuzaki and Nobuyuki Uchikoga and Takashi Ishida and Yutaka Akiyama},
  title = {Protein Complex Structure Prediction with Normal Mode Ensemble and Physical Docking},
  booktitle = {Bioinformatics week in Odaiba 2011 (BiWO2011)},
  year = 2012,
}

@inproceedings{CTT100633781,
  author = {Masahito Ohue and Yuri Matsuzaki and Nobuyuki Uchikoga and Takashi Ishida and Yutaka Akiyama},
  title = {Bound state structure estimation of protein-protein complex using rigid-body protein-protein docking method},
  booktitle = {The 10th Asia-Pacific Bioinformatics Conference (APBC2012)},
  year = 2012,
}

@inproceedings{CTT100634035,
  author = {秋山 泰 and 松崎 由理 and 内古閑 伸之 and 石田 貴士 and 大上 雅史},
  title = {網羅的タンパク質ドッキング解析プログラムMEGADOCKの開発と応用},
  booktitle = {},
  year = 2011,
}

@inproceedings{CTT100631870,
  author = {Masahito Ohue and Yuri Matsuzaki and Nobuyuki Uchikoga and Takashi Ishida and Yutaka Akiyama},
  title = {Binding Conformation Prediction of a Protein Complex Using Physical Docking},
  booktitle = {},
  year = 2011,
}

@inproceedings{CTT100633787,
  author = {内古閑 伸之 and 松崎 由理 and 大上 雅史 and 広川 貴次 and 秋山 泰},
  title = {相互作用プロファイルを用いたタンパク質間ドッキングの代表相互作用の探索},
  booktitle = {},
  year = 2011,
}

@inproceedings{CTT100631871,
  author = {Yuri Matsuzaki and Masahito Ohue and Nobuyuki Uchikoga and Takashi Ishida and Yutaka Akiyama},
  title = {MEGADOCK: a Fast Protein-protein Interaction Prediction System by Exhaustive Docking},
  booktitle = {},
  year = 2011,
}

@inproceedings{CTT100634038,
  author = {松崎由理 and 内古閑伸之 and 大上雅史 and 石田貴士 and 秋山泰},
  title = {MEGADOCK: 網羅的な立体構造のドッキングによるタンパク質間相互作用予測アプリケーション},
  booktitle = {},
  year = 2011,
}

@inproceedings{CTT100633792,
  author = {Yuri Matsuzaki and Masahito Ohue and Nobuyuki Uchikoga and Takashi Ishida and Yutaka Akiyama},
  title = {MEGADOCK: A fast protein-protein interaction prediction system by exhaustive docking},
  booktitle = {},
  year = 2011,
}

@inproceedings{CTT100624994,
  author = {山本航平 and 大上雅史 and 内古閑伸之 and 松崎由理 and 石田貴士 and 秋山 泰},
  title = {タンパク質間相互作用予測における可視化手法の開発および予測精度の改善},
  booktitle = {研究報告 バイオ情報学（BIO）},
  year = 2011,
}

@inproceedings{CTT100624993,
  author = {大上雅史 and 松崎由理 and 内古閑伸之 and 石田貴士 and 秋山 泰},
  title = {ドッキング計算に基づく網羅的タンパク質-RNA間相互作用予測},
  booktitle = {研究報告 バイオ情報学（BIO）},
  year = 2011,
}

@inproceedings{CTT100625006,
  author = {山本航平 and 大上雅史 and 松崎由理 and 石田貴士 and 秋山 泰},
  title = {タンパク質ドッキング計算結果の可視化とその解析},
  booktitle = {},
  year = 2011,
}

@inproceedings{CTT100625009,
  author = {大上雅史 and 松崎由理 and 秋山 泰},
  title = {立体構造情報を用いたドッキング計算による大規模タンパク質-RNA間相互作用予測手法},
  booktitle = {},
  year = 2011,
}

@inproceedings{CTT100619144,
  author = {松崎由理 and 内古閑伸之 and 大上雅史 and 石田貴士 and 秋山泰},
  title = {MEGADOCKを用いたタンパク質間相互作用予測のシグナル伝達系への応用},
  booktitle = {},
  year = 2011,
}

@inproceedings{CTT100619145,
  author = {Matsuzaki Yuri. and Uchikoga Nobuyuki. and Ohue Masahito. and Ishida Takashi. and Akiyama Yutaka},
  title = {Exhaustive protein-protein interaction prediction with MEGADOCK and its application to signaling pathway estimation},
  booktitle = {},
  year = 2010,
}

@inproceedings{CTT100631872,
  author = {Masahito Ohue and Yuri Matsuzaki and Yutaka Akiyama},
  title = {Development of a Protein-RNA Interaction Prediction Method Based on a Docking Calculation},
  booktitle = {},
  year = 2010,
}

@inproceedings{CTT100619146,
  author = {Matsuzaki Yuri. and Ohue Masahito. and Matsuzaki Yusuke. and Sato Toshuyuki and Akiyama Yutaka},
  title = {A computational screening system of protein-protein interactions: connecting protein structural information to biological pathway estimation},
  booktitle = {},
  year = 2010,
}

@inproceedings{CTT100876222,
  author = {大上雅史 and 松崎由理 and 松崎裕介 and 佐藤智之 and 秋山泰},
  title = {MEGADOCK：立体構造情報からの網羅的タンパク質間相互作用予測とそのシステム生物学への応用},
  booktitle = {情報処理学会論文誌数理モデル化と応用（TOM）},
  year = 2010,
}

@inproceedings{CTT100876469,
  author = {Masahito Ohue and Yuri Matsuzaki and Yusuke Matsuzaki and Toshiyuki Sato and Yutaka Akiyama},
  title = {n silico prediction of PPI network with structure-based all-to-all docking},
  booktitle = {},
  year = 2010,
}

@inproceedings{CTT100619143,
  author = {Yuri Matsuzaki},
  title = {A computational screening system of protein-protein interactions: connecting protein structural information to biological pathway estimation},
  booktitle = {},
  year = 2010,
}

@inproceedings{CTT100605237,
  author = {大上雅史 and 松崎由理 and 松崎裕介 and 佐藤智之 and 秋山泰},
  title = {MEGADOCK：立体構造情報からの網羅的タンパク質間相互作用予測とそのシステム生物学への応用},
  booktitle = {研究報告数理モデル化と問題解決（MPS）},
  year = 2010,
}

@inproceedings{CTT100600835,
  author = {大上雅史 and 松崎裕介 and 松崎由理 and 佐藤智之 and 秋山 泰},
  title = {エネルギー計算に基づくリランキングとクラスタリングを用いた網羅的タンパク質間相互作用予測手法の提案},
  booktitle = {第2回データ工学と情報マネジメントに関するフォーラム(DEIM2010)},
  year = 2010,
}

@inproceedings{CTT100604325,
  author = {松崎由理},
  title = {MEGADOCKの網羅的タンパク質相互作用予測への応用 （細菌走化性での評価、EGFRでの予備評価）},
  booktitle = {},
  year = 2010,
}

@inproceedings{CTT100604306,
  author = {Masahito Ohue and Yusuke Matsuzaki and Yuri Matsuzaki and Toshiyuki Sato and Yutaka Akiyama},
  title = {MEGADOCK: An all-to-all protein-protein interaction prediction system -- Improving the accuracy using boosting and binding energy reranking.},
  booktitle = {},
  year = 2010,
}

@inproceedings{CTT100604304,
  author = {Yuri Matsuzaki and Yusuke Matsuzaki and Masahito Ohue and Toshiyuki Sato and Yutaka Akiyama},
  title = {A computational screening system of protein-protein interactions: connecting structural information to pathway estimation.},
  booktitle = {},
  year = 2010,
}

@inproceedings{CTT100604322,
  author = {松崎裕介 and 大上雅史 and 松崎由理 and 佐藤智之 and 関嶋政和 and 秋山泰},
  title = {タンパク質の特性に基づくunboundドッキングのための剛体予測手法の改良},
  booktitle = {研究報告バイオ情報学（BIO）},
  year = 2010,
}

@inproceedings{CTT100600836,
  author = {大上雅史 and 松崎裕介 and 松崎由理 and 佐藤智之 and 秋山泰},
  title = {リランキングを用いたタンパク質ドッキングの精度向上と網羅的タンパク質間相互作用予測への応用},
  booktitle = {研究報告バイオ情報学（BIO）},
  year = 2010,
}

@inproceedings{CTT100593788,
  author = {Masahito Ohue and Yusuke Matsuzaki and Yuri Matsuzaki and Yutaka Akiyama},
  title = {Improvement of all-to-all protein-protein interaction prediction system MEGADOCK},
  booktitle = {The 20th International Conference on Genome Informatics Workshop Poster Proceedings},
  year = 2009,
}

@inproceedings{CTT100593478,
  author = {Yuri Matsuzaki and Yusuke Matsuzaki and Masahito Ohue and Toshiyuki Sato and Yutaka Akiyama},
  title = {A computational screening system of protein-protein interactions using tertiary structure data: an application to signaling pathway analysis.},
  booktitle = {Proc. BIOINFO 2009 CBI-KSBSB Joint Conference},
  year = 2009,
}

@inproceedings{CTT100593481,
  author = {Yusuke Matsuzaki and Yuri Matsuzaki and Masakazu Sekijima and Yutaka Akiyama},
  title = {Protein structure sampling based on molecular dynamics and improvement of docking prediction},
  booktitle = {Proc. BIOINFO 2009 CBI-KSBSB Joint Conference},
  year = 2009,
}

@inproceedings{CTT100593486,
  author = {Masahito Ohue and Yusuke Matsuzaki and Yuri Matsuzaki and Yutaka Akiyama},
  title = {Improvement of all-to-all protein-protein interaction prediction system MEGADOCK},
  booktitle = {Proc. BIOINFO 2009 CBI-KSBSB Joint Conference},
  year = 2009,
}

@inproceedings{CTT100589564,
  author = {Takeshi Sakurada and Moriyoshi Koizumi and Sachio Nohara and Chihiro Okada and Yuri Matsuzaki and Masaru Tomita},
  title = {E-Cell IDE: an integrated modelling and simulation environment for systems-biology},
  booktitle = {},
  year = 2009,
}

@inproceedings{CTT100589560,
  author = {Yuri Matsuzaki and Yusuke Matsuzaki and Masahito Ohue and Toshiyuki Sato and Yutaka Akiyama},
  title = {In silico screening of protein-protein interactions with all-to-all rigid docking and clustering: an application to pathway analysis},
  booktitle = {},
  year = 2009,
}

@inproceedings{CTT100590384,
  author = {松崎裕介 and 松崎由理 and 関嶋政和 and 秋山泰},
  title = {分子動力学法に基づくタンパク質構造サンプリングとドッキング予測の改良},
  booktitle = {情報処理学会研究報告},
  year = 2009,
}

@inproceedings{CTT100589920,
  author = {大上雅史 and 松崎裕介 and 松崎由理 and 秋山泰},
  title = {網羅的タンパク質間相互作用予測システムにおける判別精度の改良},
  booktitle = {研究報告バイオ情報学（BIO）},
  year = 2009,
}

@inproceedings{CTT100586434,
  author = {Yuri Matsuzaki and Yusuke Matsuzaki and Masahito Ohue and Toshiyuki Sato and Yutaka Akiyama},
  title = {A computational screening system of protein-protein interactions using tertiary structure data: with application to pathway analysis},
  booktitle = {},
  year = 2009,
}

@inproceedings{CTT100576892,
  author = {大上雅史 and 松崎裕介 and 松崎由理 and 佐藤智之 and 秋山泰},
  title = {物理化学的相互作用の導入による網羅的タンパク質間相互作用予測システムの高精度化},
  booktitle = {研究報告バイオ情報学（BIO）},
  year = 2009,
}

@inproceedings{CTT100572568,
  author = {松崎 由理 and 松崎 裕介 and 大上雅史 and 佐藤 智之 and 秋山 泰},
  title = {ドッキング後処理によるPPI検出システムの応用と評価～EGFRシグナル伝達系への適用にむけて},
  booktitle = {},
  year = 2009,
}

@inproceedings{CTT100572567,
  author = {松崎由理},
  title = {形状相補性に基づくall-to-allドッキングによる網羅的なタンパク質間相互作用予測},
  booktitle = {},
  year = 2009,
}

@inproceedings{CTT100576740,
  author = {櫻田剛史 and 小泉守義 and 野原祥夫 and 岡田千尋 and 松崎由理 and 冨田勝},
  title = {E-Cell IDE: システムバイオロジーのためのモデリング・シミュレーション統合環境},
  booktitle = {情報処理学会 研究報告},
  year = 2009,
}

@inproceedings{CTT100571802,
  author = {Yuri Matsuzaki and Yusuke Matsuzaki and Toshiyuki Sato and Yutaka Akiyama},
  title = {Virtual screening of protein-protein interactions: an application to known signal transduction systems},
  booktitle = {},
  year = 2008,
}

@inproceedings{CTT100571799,
  author = {Yutaka Akiyama and Toshiyuki Sato and Yusuke Matsuzaki and Yuri Matsuzaki},
  title = {Megadock - a rapid screening system for all-to-all protein docking analysis with precalculated fourier library of protein structures},
  booktitle = {},
  year = 2008,
}

@inproceedings{CTT100576744,
  author = {Yutaka Akiyama and Toshiyuki Sato and Yusuke Matsuzaki and Yuri Matsuzaki},
  title = {MEGADOCK - A massively parallel software system for all-to-all protein docking analysis with pre-calculated Fourier library of protein structures},
  booktitle = {},
  year = 2008,
}

@inproceedings{CTT100576738,
  author = {Yuri Matsuzaki and Yusuke Matsuzaki and Toshiyuki Sato and Yutaka Akiyama},
  title = {In silico screening method of protein-protein interactions using all-to-all rigid docking and clustering: with application to pathway analysis},
  booktitle = {},
  year = 2008,
}

@inproceedings{CTT100571815,
  author = {Yutaka Akiyama and Toshiyuki Sato and Yusuke Matsuzaki and Yuri Matsuzaki},
  title = {Megadock - a rapid screening system for all-to-all protein docking analysis with pre-calculated fourier library of protein structures},
  booktitle = {},
  year = 2008,
}

@inproceedings{CTT100571819,
  author = {Yuri Matsuzaki and Yusuke Matsuzaki and Toshiyuki Sato and Yutaka Akiyama},
  title = {Analysis of protein-protein interactions of signal transduction pathways using a docking prediction program},
  booktitle = {},
  year = 2008,
}

@inproceedings{CTT100571817,
  author = {Yusuke Matsuzaki and Yuri Matsuzaki and Toshiyuki Sato and Yutaka Akiyama},
  title = {Development of post-docking system for protein-protein interaction prediction},
  booktitle = {},
  year = 2008,
}

@inproceedings{CTT100571742,
  author = {松崎 裕介 and 松崎 由理 and 佐藤 智之 and 秋山 泰},
  title = {タンパク質間相互作用予測のためのドッキング後処理システムの開発},
  booktitle = {情報処理学会 研究報告},
  year = 2008,
}

@inproceedings{CTT100571745,
  author = {松崎 由理 and 松崎 裕介 and 佐藤 智之 and 秋山 泰},
  title = {タンパク質ドッキング予測プログラムによるシグナル伝達系のタンパク質間相互作用解析},
  booktitle = {情報処理学会 研究報告},
  year = 2008,
}

@inproceedings{CTT100571758,
  author = {秋山 泰 and 松崎 裕介 and 佐藤 智之 and 藤原 康広 and 松崎 由理 and 小西 史一},
  title = {形状相補性に基づくタンパク質間相互作用予測ソフトウェアと大規模並列計算機上での網羅的な予測環境の開発},
  booktitle = {},
  year = 2008,
}

@inproceedings{CTT100571760,
  author = {松崎 由理 and 松崎 裕介 and 佐藤 智之 and 秋山 泰},
  title = {細菌の走化性系への適用によるタンパク質間相互作用予測プログラムの評価},
  booktitle = {},
  year = 2008,
}

@inproceedings{CTT100571696,
  author = {Yuri Matsuzaki},
  title = {Modeling of signal transduction for bacterial chemotaxis using the E-Cell simulation system},
  booktitle = {},
  year = 2008,
}

@misc{CTT100619147,
  author = {Yutaka Akiyama and Yuri Matsuzaki and Nobuyuki Uchikoga and Masahito Ohue},
  title = {Exhaustive protein-protein interaction network prediction by using MEGADOCK},
  year = 2010,
}

@misc{CTT100633789,
  author = {松崎由理 and 大上雅史 and 内古閑伸之 and 石田貴士 and 秋山 泰},
  title = {MEGADOCKによるタンパク質間相互作用予測～システム生物学への応用～},
  year = 2010,
}