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Shimizu Kentaro  清水 謙多郎

… Alternative Names

清水 謙多郎  シミズ ケンタロウ

SHIMIZU Kentaro  清水 謙多郎

清水 謙太郎  シミズ ケンタロウ

Less
Researcher Number 80178970
Other IDs
  • ORCIDhttps://orcid.org/0000-0002-3245-0052
External Links
Affiliation (Current) 2025: 日本女子大学, 理学部, 教授
Affiliation (based on the past Project Information) *help 2023: 日本女子大学, 理学部, 教授
2021 – 2023: 東京大学, 大学院農学生命科学研究科(農学部), 教授
2017 – 2019: 東京大学, 大学院農学生命科学研究科(農学部), 教授
2012 – 2014: 東京大学, 農学生命科学研究科, 教授
2007 – 2011: The University of Tokyo, Graduate School of Agricultural and Life Sciences, Professor … More
2006: 東京大学, 大学院農学生命科学研究科, 教授
1998 – 2005: 東京大学, 大学院・農学生命科学研究科, 教授
1996 – 1997: 東京大学, 大学院・農学生命科学研究科, 助教授
1994 – 1995: 電気通信大学, 電気通信学部, 助教授
1992: 電気通信大学, 電気通信学部, 助教授
1990: Univ. Electro-Comm., Fac. E-C., Assoc. Prof., 電気通信学部, 助教授
1990: 電気通信大学, 電気通信学部, 講師 Less
Review Section/Research Field
Principal Investigator
Biological Sciences / 計算機科学 / Science and Engineering / Bioinformatics/Life informatics / Life / Health / Medical informatics / Basic Section 62010:Life, health and medical informatics-related
Except Principal Investigator
Basic Section 62010:Life, health and medical informatics-related / Informatics
Keywords
Principal Investigator
構造予測 / タンパク質 / 生体生命情報学 / 並列計算 / プロテオーム / 蛋白質 / バイオインフォマティクス / グリッドコンピューティング / 資源管理 / MPI … More / 分子動力学法 / ミドルウェア / 分散共有メモリ / 統計ポテンシャル / 科学技術計算 / スケジューリング / 並列プログラミング環境 / オペレーティングシステム / scheduling / 分子間相互作用 / BLOSUM / アミノ酸配列 / 分子動力学シミュレーション / プロセッサ割当て / 大規模並列システム / 深層学習 / bioinformatics / computational chemistry / molecular dynamics / processor allocation / parallel programming environment / parallel computing / 大規模並列計算機 / 計算化学 / 分子動力学計算 / プロセス間通信 / operating system / 保護 / マイクロカーネル / 分散処理 / オブジェクト指向 / 構造精密化 / 構造評価 / 分子動力学 / 複合体 / 機能予測 / フラグメントアセンブリ方式 / ホモロジーモデリング / 遺伝子クラスタリング / 二次構造 / 分散共有記憶 / 負荷分散 / スレッド / カーネル / PSSM / MoRF / 天然変性 / 分子シミュレーション / ドッキング予測 / ペプチド設計 / 抗ウィルスペプチド / 活性予測 / 機械学習 / 抗菌性 / ペプチド / molecular dynamics simulation / protein structure assessment / protein structure refinement / protein structure prediction / proteome / 蛋白質構造評価 / 蛋白質構造精密化 / 蛋白質構造予測 / grid computing / data consistency protocol / scientific computing / distributed shared memory / Parallel programming environment / データー貫性制御 / データ一貫性制御 / 生命情報科学 / MP1 / エネルギー最小化計算 / 分子動力学シュミレーション / 動的資源管理 / MPI (Message Passing Interface) / スレープ方式 / マスタ / 空間分割法 / thread / object oriented system / kernel / ページ置換え方針 / global page placement / global scheduling / load balancing / multiprocessor systems / responsiveness / real-time processing / フォールトトレラント / 超並列計算機 / エミュレーション / 仮想記憶 / 並列処理 / 大域的ページ配置方針 / 大域的スケジューリング / 耐故障性 / 実時間処理 / microkernel / distributed processing / abstract data type / obejct-orient system / 永続処理 / 抽象データ型 / 予測機能 / 相互作用 / 糖 / データベース / 相互作用予測 / 糖鎖 / ブロテオーム / 不規則領域 / ネットワーク / ソフトウェア学 / ハイパフォーマンス・コンピューティング / マルチカノニカル法 / アビニシオ法 / 構造クラスタリング / ab initio法 / 配列類似度 / ハードウェア適応性 / 超並列処理 … More
Except Principal Investigator
新生ペプチド / 翻訳制御 / 粗視化モデル / 分子動力学シミュレーション / AMBER / ドッキングシミュレーション / Martini / 粗視化 / 翻訳アレスト / ドッキング / シミュレーション / uORF / リボソーム / Computer Network / Light-Weight Process / Process Migration / Parametric Analysis / Load Balancing Algorithm / Optimal Load Balancing / Distributed Computer System / Distributed Operating System / コンピュ-タ・ネットワ-ク / プロセス・マイグレ-ション / 分散透明性 / コンピュ-タネットワ-ク / 重さ可変プロセス / プロセス移送 / 負荷分散アルゴリズム / 最適負荷分散 / 分散処理 / 分散型コンピュ-タシステム / 分散型オペレ-ティングシステム / 並列計算環境 / 大規模並列計算機 / 分子動力学法 / 分子シミュレーション / 尿素 / 変性剤 / 疎水性相互作用 / 疎水効果 Less
  • Research Projects

    (29 results)
  • Research Products

    (90 results)
  • Co-Researchers

    (21 People)
  •  非コード領域・タンパク構造情報を含むオミクス統合解析に基づく精密医療の実現

    • Principal Investigator
      高橋 広夫
    • Project Period (FY)
      2021 – 2023
    • Research Category
      Grant-in-Aid for Scientific Research (B)
    • Review Section
      Basic Section 62010:Life, health and medical informatics-related
    • Research Institution
      Kanazawa University
  •  Computational Prediction and Experimental Validation of the Regulatory Mechanisms of Functional Peptides Encoded in Genomic Junk Regions

    • Principal Investigator
      Shuichi Fukuyoshi
    • Project Period (FY)
      2021 – 2023
    • Research Category
      Grant-in-Aid for Scientific Research (C)
    • Review Section
      Basic Section 62010:Life, health and medical informatics-related
    • Research Institution
      Kanazawa University
  •  Docking prediction and design of peptides by molecluar simulation and deep learningPrincipal Investigator

    • Principal Investigator
      清水 謙多郎
    • Project Period (FY)
      2021 – 2024
    • Research Category
      Grant-in-Aid for Scientific Research (C)
    • Review Section
      Basic Section 62010:Life, health and medical informatics-related
    • Research Institution
      Japan Women's University
      The University of Tokyo
  •  Prediction and analysis of intrinsically disordered regions in membrane proteinsPrincipal Investigator

    • Principal Investigator
      清水 謙多郎
    • Project Period (FY)
      2017 – 2019
    • Research Category
      Grant-in-Aid for JSPS Fellows
    • Research Field
      Life / Health / Medical informatics
    • Research Institution
      The University of Tokyo
  •  Development of protein-carbohydrate binding prediction systems and databasesPrincipal Investigator

    • Principal Investigator
      SHIMIZU Kentaro
    • Project Period (FY)
      2011 – 2014
    • Research Category
      Grant-in-Aid for Scientific Research (B)
    • Research Field
      Bioinformatics/Life informatics
    • Research Institution
      The University of Tokyo
  •  タンパク質相互作用のネットワーク予測から原子レベルの結合予測までの統合的研究Principal Investigator

    • Principal Investigator
      清水 謙太郎 (清水 謙多郎)
    • Project Period (FY)
      2008 – 2010
    • Research Category
      Grant-in-Aid for Scientific Research on Priority Areas
    • Review Section
      Biological Sciences
    • Research Institution
      The University of Tokyo
  •  Database Development and Functional Analysis of Protein Disorder RegionsPrincipal Investigator

    • Principal Investigator
      SHIMIZU Kentaro
    • Project Period (FY)
      2008 – 2010
    • Research Category
      Grant-in-Aid for Scientific Research (C)
    • Research Field
      Bioinformatics/Life informatics
    • Research Institution
      The University of Tokyo
  •  高精度のドッキング機能を有するタンパク質間相互作用予測システムの開発Principal Investigator

    • Principal Investigator
      清水 謙多郎
    • Project Period (FY)
      2006 – 2007
    • Research Category
      Grant-in-Aid for Scientific Research on Priority Areas
    • Review Section
      Biological Sciences
    • Research Institution
      The University of Tokyo
  •  高精度のドッキング機能を有するタンパク質間相互作用予測システムの開発Principal Investigator

    • Principal Investigator
      清水 謙多郎
    • Project Period (FY)
      2005
    • Research Category
      Grant-in-Aid for Scientific Research on Priority Areas
    • Review Section
      Biological Sciences
    • Research Institution
      The University of Tokyo
  •  Development of methods for high-resolution protein structure modeling and for model structure assessmentPrincipal Investigator

    • Principal Investigator
      SHIMIZU Kentaro
    • Project Period (FY)
      2005 – 2007
    • Research Category
      Grant-in-Aid for Scientific Research (C)
    • Research Field
      Bioinformatics/Life informatics
    • Research Institution
      The University of Tokyo
  •  ホモロジーモデリングとアビニシオ法の統合による高精度タンパク質構造予測手法の開発Principal Investigator

    • Principal Investigator
      清水 謙多郎
    • Project Period (FY)
      2004
    • Research Category
      Grant-in-Aid for Scientific Research on Priority Areas
    • Review Section
      Biological Sciences
    • Research Institution
      The University of Tokyo
  •  大規模分散データの真に透過で効率的な共有を実現する分散共有配列システムの開発Principal Investigator

    • Principal Investigator
      清水 謙多郎
    • Project Period (FY)
      2004 – 2005
    • Research Category
      Grant-in-Aid for Scientific Research on Priority Areas
    • Review Section
      Science and Engineering
    • Research Institution
      The University of Tokyo
  •  ホモロジーモデリングとアビニシオ法の統合による高精度タンパク質構造予測手法の開発Principal Investigator

    • Principal Investigator
      清水 謙多郎
    • Project Period (FY)
      2003
    • Research Category
      Grant-in-Aid for Scientific Research on Priority Areas
    • Review Section
      Biological Sciences
    • Research Institution
      The University of Tokyo
  •  大規模分散データの効率的な共有を実現する並列コンピューティング環境の開発Principal Investigator

    • Principal Investigator
      清水 謙多郎
    • Project Period (FY)
      2003
    • Research Category
      Grant-in-Aid for Scientific Research on Priority Areas
    • Review Section
      Science and Engineering
    • Research Institution
      The University of Tokyo
  •  タンパク質の局所構造情報を利用したab initio立体構造・機能予測手法の開発Principal Investigator

    • Principal Investigator
      清水 謙多郎
    • Project Period (FY)
      2002
    • Research Category
      Grant-in-Aid for Scientific Research on Priority Areas
    • Review Section
      Biological Sciences
    • Research Institution
      The University of Tokyo
  •  大規模分散データの効率的な共有を実現する並列コンピューティング環境の開発Principal Investigator

    • Principal Investigator
      清水 謙多郎
    • Project Period (FY)
      2002
    • Research Category
      Grant-in-Aid for Scientific Research on Priority Areas
    • Review Section
      Science and Engineering
    • Research Institution
      The University of Tokyo
  •  タンパク質の局所構造情報を利用したab initio立体構造・機能予測手法の開発Principal Investigator

    • Principal Investigator
      清水 謙多郎
    • Project Period (FY)
      2001
    • Research Category
      Grant-in-Aid for Scientific Research on Priority Areas (C)
    • Review Section
      Biological Sciences
    • Research Institution
      The University of Tokyo
  •  大規模分散データの効率的な共有を実現する並列コンピューティング環境の開発Principal Investigator

    • Principal Investigator
      清水 謙多郎
    • Project Period (FY)
      2001
    • Research Category
      Grant-in-Aid for Scientific Research on Priority Areas (C)
    • Review Section
      Science and Engineering
    • Research Institution
      The University of Tokyo
  •  Development of a Parallel Programming Environment based on Distributed Shared Arrays with Application-Specific Resource ManagementPrincipal Investigator

    • Principal Investigator
      SHIMIZU Kentaro
    • Project Period (FY)
      2001 – 2003
    • Research Category
      Grant-in-Aid for Scientific Research (C)
    • Research Field
      計算機科学
    • Research Institution
      The University of Tokyo
  •  タンパク質の局所構造情報を利用したab initio立体構造・機能予測手法の開発Principal Investigator

    • Principal Investigator
      清水 謙多郎
    • Project Period (FY)
      2000
    • Research Category
      Grant-in-Aid for Scientific Research on Priority Areas (C)
    • Review Section
      Biological Sciences
    • Research Institution
      The University of Tokyo
  •  Development of a Parallel Programming Environment with Dynamic Resource Management FacilitiesPrincipal Investigator

    • Principal Investigator
      SHIMIZU Kentaro
    • Project Period (FY)
      1999 – 2001
    • Research Category
      Grant-in-Aid for Scientific Research (B)
    • Research Field
      計算機科学
    • Research Institution
      THE UNIVERSITY OF TOKYO
  •  ハードウェア構成に柔軟に適応する資源管理機能を備えた並列プログラミング環境の開発Principal Investigator

    • Principal Investigator
      清水 謙多郎
    • Project Period (FY)
      1998
    • Research Category
      Grant-in-Aid for Scientific Research on Priority Areas (A)
    • Research Institution
      The University of Tokyo
  •  蛋白質の安定性・折れたたみ機構における水・変性剤の分子メカニズム

    • Principal Investigator
      池口 満徳
    • Project Period (FY)
      1998
    • Research Category
      Grant-in-Aid for Scientific Research on Priority Areas (A)
    • Research Institution
      The University of Tokyo
  •  Efficient Processor Allocation Policies for Massively Parallel SystemsPrincipal Investigator

    • Principal Investigator
      SHIMIZU Kentaro
    • Project Period (FY)
      1998 – 2000
    • Research Category
      Grant-in-Aid for Scientific Research (C)
    • Research Field
      計算機科学
    • Research Institution
      THE UNIVERSITY OF TOKYO
  •  Study on operating system architectures for supporting application-specific resource managementPrincipal Investigator

    • Principal Investigator
      SHIMIZU Kentaro
    • Project Period (FY)
      1996 – 1997
    • Research Category
      Grant-in-Aid for Scientific Research (C)
    • Research Field
      計算機科学
    • Research Institution
      The University of Tokyo
  •  Development of a responsive operating system for scalable multiprocessor systemsPrincipal Investigator

    • Principal Investigator
      SHIMIZU Kentaro
    • Project Period (FY)
      1995 – 1997
    • Research Category
      Grant-in-Aid for Scientific Research (A)
    • Research Field
      計算機科学
    • Research Institution
      The University of Tokyo
      The University of Electro-Communications
  •  Development of an operating system that supports the distributed and persistent light-weight objectsPrincipal Investigator

    • Principal Investigator
      SHIMIZU Kentaro
    • Project Period (FY)
      1994 – 1995
    • Research Category
      Grant-in-Aid for General Scientific Research (C)
    • Research Field
      計算機科学
    • Research Institution
      The University of Electro-Communications
  •  超並列オペレーティングシステムにおける負荷分散および分散記憶管理の研究Principal Investigator

    • Principal Investigator
      清水 謙多郎
    • Project Period (FY)
      1992
    • Research Category
      Grant-in-Aid for Scientific Research on Priority Areas
    • Research Institution
      The University of Electro-Communications
  •  Research on the Design of Distributed Operating Systems

    • Principal Investigator
      KAMEDA Hisao
    • Project Period (FY)
      1989 – 1990
    • Research Category
      Grant-in-Aid for General Scientific Research (B)
    • Research Field
      Informatics
    • Research Institution
      The University of Electro-Communications

All 2024 2023 2022 2021 2019 2018 2015 2014 2013 2011 2010 2009 2008 2007 2006 2005 Other

All Journal Article Presentation Book

  • [Book] タンパク質構造解析手法とIn silicoスクリーニングへの応用(第5章, 第1節)2023

    • Author(s)
      清水謙多郎
    • Total Pages
      530
    • Publisher
      技術情報協会
    • ISBN
      9784861049958
    • Data Source
      KAKENHI-PROJECT-21K12122
  • [Book] Web連携テキスト バイオインフォマティクス 基礎と応用2022

    • Author(s)
      門田幸二, 清水謙多郎, 岸野洋久, 寺田透
    • Total Pages
      228
    • Publisher
      培風館
    • ISBN
      9784563078324
    • Data Source
      KAKENHI-PROJECT-21K12122
  • [Book] 中国科学技術月報第44号中国・日本科学最前線-研究の現場から-2011年版(タンパク質の構造予測手法の開発)2011

    • Author(s)
      清水謙多郎
    • Publisher
      科学技術振興機構中国総合研究センター
    • Data Source
      KAKENHI-PROJECT-20500269
  • [Book] 遺伝子医学MOOK14次世代創薬テクノロジー実践:インシリコ創薬の最前線(タンパク質のabinitio構造予測)2009

    • Author(s)
      中村周吾,清水謙多郎
    • Publisher
      メディカルドゥ
    • Data Source
      KAKENHI-PROJECT-20500269
  • [Journal Article] QM/MM Study of the Catalytic Mechanism and Substrate Specificity of the Aromatic Substrate C-Methyltransferase Fur62024

    • Author(s)
      Zhao Fan、Moriwaki Yoshitaka、Noguchi Tomohiro、Shimizu Kentaro、Kuzuyama Tomohisa、Terada Tohru
    • Journal Title

      Biochemistry

      Volume: 63 Issue: 6 Pages: 806-814

    • DOI

      10.1021/acs.biochem.3c00556

    • Peer Reviewed / Open Access
    • Data Source
      KAKENHI-PROJECT-21K12122, KAKENHI-PLANNED-22H05120, KAKENHI-PLANNED-22H05126
  • [Journal Article] Enhanced clustering-based differential expression analysis method for RNA-seq data2023

    • Author(s)
      Makino M, Shimizu K, Kadota K.
    • Journal Title

      MethodsX

      Volume: 12 Pages: 102518-102518

    • DOI

      10.1016/j.mex.2023.102518

    • Peer Reviewed / Open Access
    • Data Source
      KAKENHI-PROJECT-21K12120, KAKENHI-PROJECT-21K12122
  • [Journal Article] Comprehensive computational analysis of the SRK-SP11 molecular interaction underlying self-incompatibility in Brassicaceae using improved structure prediction for cysteine-rich proteins2023

    • Author(s)
      Sawa Tomoki、Moriwaki Yoshitaka、Jiang Hanting、Murase Kohji、Takayama Seiji、Shimizu Kentaro、Terada Tohru
    • Journal Title

      Computational and Structural Biotechnology Journal

      Volume: 21 Pages: 5228-5239

    • DOI

      10.1016/j.csbj.2023.10.026

    • Peer Reviewed / Open Access / Int'l Joint Research
    • Data Source
      KAKENHI-PROJECT-21K12122, KAKENHI-PROJECT-21K06110, KAKENHI-PROJECT-21H05030
  • [Journal Article] Feedback-AVPGAN: Feedback-guided generative adversarial network for generating antiviral peptides2022

    • Author(s)
      1.Kano Hasegawa, Yoshitaka Moriwaki, Tohru Terada, Cao Wei, Kentaro Shimizu
    • Journal Title

      Journal of Bioinformatics and Computational Biology

      Volume: 20 Issue: 06 Pages: 2250026-2250026

    • DOI

      10.1142/s0219720022500263

    • Peer Reviewed / Open Access / Int'l Joint Research
    • Data Source
      KAKENHI-PROJECT-21K12122
  • [Journal Article] Prediction of MoRFs Based on n-gram Convolutional Neural Network2019

    • Author(s)
      Chun Fang, Yoshitaka Moriwaki, Caihong Li, and Kentaro Shimizu
    • Journal Title

      Proceedings of 11th International Conferenceon Bioinformatics and Computational Biology

      Volume: 60 Pages: 113-119

    • DOI

      10.29007/5k4z

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-17F17050
  • [Journal Article] Prediction of Antifungal Peptides by Deep Learning with Character Embedding2019

    • Author(s)
      Chun Fang, Yoshitaka Moriwaki, Caihong Li, and Kentaro Shimizu
    • Journal Title

      IPSJ Transactions on Bioinformatics

      Volume: 12 Issue: 0 Pages: 21-29

    • DOI

      10.2197/ipsjtbio.12.21

    • NAID

      130007685780

    • ISSN
      1882-6679
    • Language
      English
    • Peer Reviewed / Open Access / Int'l Joint Research
    • Data Source
      KAKENHI-PROJECT-17F17050
  • [Journal Article] Comparative analysis of membrane protein structure databases2018

    • Author(s)
      K. Shimizu, W. Cao, G. Saad, M. Shoji, T. Terada
    • Journal Title

      BBA - Biomembranes

      Volume: 1860 Issue: 5 Pages: 1077-1091

    • DOI

      10.1016/j.bbamem.2018.01.005

    • Peer Reviewed / Open Access / Int'l Joint Research
    • Data Source
      KAKENHI-PROJECT-17F17050
  • [Journal Article] Identifying MoRFs in Disordered Protein Using Enlarged Conserved Features2018

    • Author(s)
      Chun Fang, Yoshitaka Moriwaki, Daming Zhu, and K. Shimizu
    • Journal Title

      2018 6th International Conference on Bioinformatics and Computational Biology

      Volume: 12 Pages: 50-54

    • DOI

      10.1145/3194480.3198908

    • Peer Reviewed / Open Access
    • Data Source
      KAKENHI-PROJECT-17F17050
  • [Journal Article] Overdominance effect of the bovine ghrelin receptor (GHSR1a)-DelR242 locus on growth in Japanese Shorthorn weaner bulls: Heterozygote advantage in bull selection and molecular mechanisms.2015

    • Author(s)
      Masanori Komatsu, Yoichi Sato, Tatsuki Negami, Tohru Terada, Osamu Sasaki, Jumpei Yasuda, Aisaku Arakawa, Chikara Yoshida, Hideaki Takahashi, Aduli E.O. Malau-Aduli, Keiichi Suzuki and Kentaro Shimizu
    • Journal Title

      G3: Genes, Genomes, Genetics

      Volume: Volume 5 Issue: 2 Pages: 271-279

    • DOI

      10.1534/g3.114.016105

    • Peer Reviewed / Open Access
    • Data Source
      KAKENHI-PROJECT-23300109
  • [Journal Article] Linked Open Data Construction of Purpose Oriented Interactomics by Integration of Life Sciences LOD2014

    • Author(s)
      込山 悠介, 番野 雅城, 鑓水 優行, 加藤 文彦, 大向 一輝, 武田 英明, 清水 謙多郎
    • Journal Title

      Transactions of the Japanese Society for Artificial Intelligence

      Volume: 29 Issue: 4 Pages: 356-363

    • DOI

      10.1527/tjsai.29.356

    • NAID

      130004927341

    • ISSN
      1346-0714, 1346-8030
    • Language
      Japanese
    • Peer Reviewed / Acknowledgement Compliant / Open Access
    • Data Source
      KAKENHI-PROJECT-23300109
  • [Journal Article] Structural Basis of the Divergent Oxygenation Reactions Catalyzed by the Rieske Nonheme Iron Oxygenase Carbazole 1,9a-Dioxygenase2014

    • Author(s)
      Kengo Inoue, Yusuke Usami, Yuji Ashikawa, Haruko Noguchi, Takashi Umeda, Aiko Yamagami-Ashikawa, Tadafumi Horisaki, Hiromasa Uchimura, Tohru Terada, Shugo Nakamura, Kentaro Shimizu, Hiroshi Habe, Hisakazu Yamane, Zui Fujimoto and Hideaki Nojiri
    • Journal Title

      Applied and Environmental Microbiology

      Volume: Volume 80 Issue: 9 Pages: 2821-2832

    • DOI

      10.1128/aem.04000-13

    • Peer Reviewed / Open Access
    • Data Source
      KAKENHI-PROJECT-23300109, KAKENHI-PROJECT-24780076, KAKENHI-PROJECT-26850052
  • [Journal Article] Coarse-Grained Molecular Dynamics Simulations of Protein-Ligand Binding2014

    • Author(s)
      Tatsuki Negami, Kentaro Shimizu, Tohru Terada
    • Journal Title

      Journal of Computational Chemistry

      Volume: Volume 35 Issue: 25 Pages: 1835-1845

    • DOI

      10.1002/jcc.23693

    • Peer Reviewed / Open Access
    • Data Source
      KAKENHI-PROJECT-23300109, KAKENHI-PROJECT-24570179
  • [Journal Article] Engineering the allosteric properties of archaeal non-phosphorylating glyceraldehyde-3-phosphate dehydrogenases.2014

    • Author(s)
      Fumiaki Ito, Masayuki Miyake, Shinya Fushinobu, Shugo Nakamura, Kentaro Shimizu, Takayoshi Wakagi
    • Journal Title

      BBA - Proteins and Proteomics

      Volume: Volume 1844 Issue: 4 Pages: 759-766

    • DOI

      10.1016/j.bbapap.2014.01.017

    • Peer Reviewed / Open Access
    • Data Source
      KAKENHI-PROJECT-23300109, KAKENHI-PROJECT-24580136
  • [Journal Article] TCC: an R package for comparing tag count data with robust normalization strategies.2013

    • Author(s)
      Sun, J., Nishiyama, T., Shimizu, K., and Kadota, K.
    • Journal Title

      BMC Bioinformatics

      Volume: 14 Issue: 1 Pages: 219-219

    • DOI

      10.1186/1471-2105-14-219

    • Peer Reviewed / Acknowledgement Compliant / Open Access
    • Data Source
      KAKENHI-PLANNED-22128008, KAKENHI-PROJECT-23300109, KAKENHI-PROJECT-24500359
  • [Journal Article] Selective binding of antimicrobial porphyrins to the hame-receptor IsdH-NEAT3 of Staphylococcus aureus.2013

    • Author(s)
      Nhuan Vu
    • Journal Title

      Protein Science

      Volume: 22 Issue: 7 Pages: 942-953

    • DOI

      10.1002/pro.2276

    • Peer Reviewed / Open Access
    • Data Source
      KAKENHI-PROJECT-13J06526, KAKENHI-PROJECT-23300109, KAKENHI-PROJECT-24000011, KAKENHI-PROJECT-25249115
  • [Journal Article] Heme binding mechanism of structurally similar iron-regulated surface determinant near transporter domains of Staphylococcus aureus exhibiting different affinities for heme.2013

    • Author(s)
      Yoshitaka Moriwaki
    • Journal Title

      Biochemistry

      Volume: 52 Issue: 49 Pages: 8866-8877

    • DOI

      10.1021/bi4008325

    • Peer Reviewed / Open Access
    • Data Source
      KAKENHI-PROJECT-13J06526, KAKENHI-PROJECT-23300109, KAKENHI-PROJECT-24000011, KAKENHI-PUBLICLY-24102516, KAKENHI-PROJECT-25249115, KAKENHI-PROJECT-25708026
  • [Journal Article] タンパク質の構造予測手法の開発2011

    • Author(s)
      清水謙多郎
    • Journal Title

      科学技術振興機構中国科学技術月報

      Pages: 137-140

    • Data Source
      KAKENHI-PROJECT-20500269
  • [Journal Article] Protein-Protein Docking Using Multi-layered Spherical Basis Functions2011

    • Author(s)
      K.Sumikoshi, T.Terada, S.Nakamura, K.Shimizu
    • Journal Title

      Proceedings of the 2011 International Conference on Bioscience, Biochemistry and Bioinformatics

      Pages: 342-347

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-20500269
  • [Journal Article] Prediction of carbohydrate-binding proteins from sequences using support vector machines.2010

    • Author(s)
      S.Someya, M.Kakuta, M.Morita, K.Sumikoshi, W.Cao, Z.Ge, O.Hirose, S.Nakamura, T.Terada, K.Shimizu
    • Journal Title

      Advances in Bioinformatics

      Pages: 289301-289301

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-20500269
  • [Journal Article] Computational Protocol for Screening GPI-anchored Proteins2009

    • Author(s)
      Cao Wei, Kazuya Sumikoshi, Tohru Terada, Shugo Nakamura, Katsuhiko Kitamoto, Kentaro Shimizu
    • Journal Title

      Proceedings of the First International ConBerence onBioinlbrmatics and Computational Biology (掲載確定)

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-20016006
  • [Journal Article] Accurate prediction of native tertiary structure of protein using molecular dynamics simulation with the aid of the knowledge of secondary structures2009

    • Author(s)
      Tadaomi Furuta, Kentaro Shimizu, Tohru Terada
    • Journal Title

      Chemical Physics Letters 472

      Pages: 134-139

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-20016006
  • [Journal Article] Accurate prediction of native tertiary structure of protein using molecular dynamics simulation with the aid of the knowledge of secondary structures2009

    • Author(s)
      Tadaomi Furuta, Kentaro Shimizu,Tohru Terada
    • Journal Title

      Chemical Physics Letters 472

      Pages: 134-139

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-20500269
  • [Journal Article] Comprehensive analysis of sequence-structure relationships in the loop regions of proteins2009

    • Author(s)
      S.Nakamura, K.Shimizu
    • Journal Title

      GIW 2009 23

      Pages: 106-116

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-20500269
  • [Journal Article] Computational Protocol for Screening GPI-anchored Proteins, Proceedings of the First International Conference on Bioinformatics and Computational Biology (BICoB)2009

    • Author(s)
      W.Cao, K.Sumikoshi, T.Terada, S.Nakamura, K.Kitamoto, K.Shimizu
    • Journal Title

      Springer Lecture Notes in Bioinformatics Series 5462

      Pages: 164-175

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-20500269
  • [Journal Article] Accurate prediction of native tertiary structure of protein using molecular dynamics simulation with the aid of the knowledge of secondary structures2009

    • Author(s)
      T.Furuta, K.Shimizu, T.Terada
    • Journal Title

      Chemical Physics Letters 472

      Pages: 134-139

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-20500269
  • [Journal Article] Refinement of comparative models of protein structure by using multicanonical molecular dynamics simulations2008

    • Author(s)
      R.Ishitani, T.Terada, K.Shimizu
    • Journal Title

      Molecular Simulation 34

      Pages: 327-336

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-20500269
  • [Journal Article] Prediction of protein-protein interaction sites using only sequence information and using both sequence and structural information2008

    • Author(s)
      M.Kakuta, S.Nakamura, K.Shimizu
    • Journal Title

      IPSJ Transactions on Bioinformatics 49

      Pages: 25-35

    • NAID

      110006684907

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-20500269
  • [Journal Article] Highly accurate method for ligand-binding site prediction in unbound state (apo) protein structures2008

    • Author(s)
      Mizuki Morita, Shugo Nakamura, Kentaro Shimizu
    • Journal Title

      PROTEINS : Structure, Function, and Bioinformatics 73

      Pages: 468-479

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-20016006
  • [Journal Article] Refinement of comparative models of protein structure by using multicanonical molecular dynamics simulations2008

    • Author(s)
      Ryuuchiro Ishitani, Tohru Terada, Kehtaro Shimizu
    • Journal Title

      Molecular Simulation 34

      Pages: 327-336

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-20500269
  • [Journal Article] A compahson of generahzed Born methods in folding simulations2008

    • Author(s)
      Tohru Terada, Kentaro Shimizu
    • Journal Title

      Chemical Physics Letters 460

      Pages: 295-299

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-20500269
  • [Journal Article] Highly accurate method for ligand-binding site prediction in unbound state (apo) protein structures2008

    • Author(s)
      M.Morita, S.Nakamura, K.Shimizu
    • Journal Title

      PROTEINS: Structure, Function, and Bioinformatics 73, 2

      Pages: 468-479

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-20500269
  • [Journal Article] IgE^b immune complexes activate macrophages through Fc ^γRIV binding2007

    • Author(s)
      Masayuki Hirano, Randall S. Davis, W. David Fine, Shugo Nakamura, Kentaro Shimizu, Hirokazu Yagi, Koichi Kato, Robert P. Stephan, Max D. Cooper
    • Journal Title

      Nature Immunology 8

      Pages: 762-771

    • Description
      「研究成果報告書概要(欧文)」より
    • Data Source
      KAKENHI-PROJECT-17500191
  • [Journal Article] Mechanism of the difference in the binding affinity of E.coli tRNAGln to glutaminyl-tRNA synthetase caused by non-interface nucleotides in variable loop2007

    • Author(s)
      Satoshi Yamazaki, Shugo Nakamura, Tohru Terada, Kentaro Shimizu
    • Journal Title

      Biophysical Journal 92

      Pages: 192-200

    • Description
      「研究成果報告書概要(欧文)」より
    • Data Source
      KAKENHI-PROJECT-17500191
  • [Journal Article] Folding free-energy landscape of a 10-residue mini-protein, chignolin2006

    • Author(s)
      Daisuke Satoh, Tohru Terada, Shugo Nakamura, Kentaro Shimizu
    • Journal Title

      FEBS Letters 580

      Pages: 3422-3426

    • Description
      「研究成果報告書概要(欧文)」より
    • Data Source
      KAKENHI-PROJECT-17500191
  • [Journal Article] A multicanonical ab initio molecular dynamics method : application to conformation sampling of alanine tripeptide2006

    • Author(s)
      Ryota Jono, Tohru Terada, Kentaro Shimizu
    • Journal Title

      Chemical Physics Letters 432

      Pages: 306-312

    • Description
      「研究成果報告書概要(欧文)」より
    • Data Source
      KAKENHI-PROJECT-17500191
  • [Journal Article] Insight of the Signal Motif of GPI-(like)-anchored Proteins by Using SVM2006

    • Author(s)
      Wei Cao, Kazuya Sumikoshi, Tohru Terada, Shugo Nakamura, Kentaro Shimizu
    • Journal Title

      Proceedings of the 2006 International Conference on Bioinformatics and Computational Biology(BIOCOMP'06)

      Pages: 541-546

    • Description
      「研究成果報告書概要(欧文)」より
    • Data Source
      KAKENHI-PROJECT-17500191
  • [Journal Article] Potential for Assessing Quality of Protein Structure hated on Contact Number Prediction2006

    • Author(s)
      Takashi Ishida, Shugo Nakamura, Kentaro Shimizu
    • Journal Title

      PROTEINS : Structure, Function, and Bioinformatics 64, 4

      Pages: 940-947

    • Description
      「研究成果報告書概要(欧文)」より
    • Data Source
      KAKENHI-PROJECT-17500191
  • [Journal Article] Evaluation of efficiency of reference potential spatial warping algorithm in conformational sampling of peptides2006

    • Author(s)
      Ryuichiro Ishitani, Tohru Terada, Kentaro Shimizu
    • Journal Title

      Journal of Chemical Physics 124

      Pages: 214902-214902

    • Description
      「研究成果報告書概要(欧文)」より
    • Data Source
      KAKENHI-PROJECT-17500191
  • [Journal Article] High-precision Geometric Modeling of 3D Artifacts for Virtual Restoration2006

    • Author(s)
      Junta Doi, Kentaro Shimizu, Wataru Sato, Shinji Morishita
    • Journal Title

      Proceedings of the IEEE International Conference on Virtual Environments, Human-computer Interfaces, and Measurement Systems

      Pages: 136-141

    • Description
      「研究成果報告書概要(欧文)」より
    • Data Source
      KAKENHI-PROJECT-17500191
  • [Journal Article] Identification of GPI-(like) -anchored Proteins by using SVM2006

    • Author(s)
      Wei Cao, Kentaro Shimizu
    • Journal Title

      Proceedings of the First International Multi-symposiums of Computer Science and Computational Sciences(IMSCCS'06)

      Pages: 711-715

    • Description
      「研究成果報告書概要(欧文)」より
    • Data Source
      KAKENHI-PROJECT-17500191
  • [Journal Article] A fast protein-protein docking algorithm using series expansion in terms of spherical basis functions2005

    • Author(s)
      Kazuya Sumikoshi, Tohru Terada, Shugo Nakamura, Kentaro Shimizu
    • Journal Title

      Proceedings of the 16th International Conference on Genome Informatics(GIW2005) 16

      Pages: 161-173

    • NAID

      130003997422

    • Description
      「研究成果報告書概要(欧文)」より
    • Data Source
      KAKENHI-PROJECT-17500191
  • [Journal Article] Highly accurate method for ligand-binding site prediction in unbound state(apo) protein structures

    • Author(s)
      Mizuki Morita, Shugo Nakamura, Kentaro Shimizu
    • Journal Title

      PROTEINS : Structure, Function, and Bioinformatics, accepted

    • Description
      「研究成果報告書概要(欧文)」より
    • Data Source
      KAKENHI-PROJECT-17500191
  • [Journal Article] Understanding the roles of amino acid residues in tertiary structure formation of chignolin by using molecular dynamics simulation

    • Author(s)
      Tohru Terada, Daisuke Satoh, Tsutomu Mikawa, Yutaka Ito, Kentaro Shimizu
    • Journal Title

      PROTEINS : Structure, Function, and Bioinformatics, accepted

    • Description
      「研究成果報告書概要(欧文)」より
    • Data Source
      KAKENHI-PROJECT-17500191
  • [Journal Article] Refinement of comparative models of protein structure by using multicanonical molecular dynamics simulations

    • Author(s)
      Ryuichiro Ishitani, Tohru Terada, Kentaro Shimizu
    • Journal Title

      Molecular Simulation 34, 3

      Pages: 327-336

    • Description
      「研究成果報告書概要(欧文)」より
    • Data Source
      KAKENHI-PROJECT-17500191
  • [Presentation] 光合成反応中心-光捕集アンテナ超分子複合体におけるユビキノン/ユビキノール移動経路の解明2023

    • Author(s)
      Yosuke Teshirogi, Yoshitaka Moriwaki, Kentaro Shimizu, Tohru Terada
    • Organizer
      日本生物物理学会
    • Data Source
      KAKENHI-PROJECT-21K12122
  • [Presentation] 生成モデルのよるタンパク質距離行列及び立体構造の生成2023

    • Author(s)
      Ryo Okada, Yoshitaka Moriwaki, Kentaro Shimizu, Tohru Terada
    • Organizer
      日本生物物理学会
    • Data Source
      KAKENHI-PROJECT-21K12122
  • [Presentation] Prediction of antihypertensive activity of peptides using machine learning2022

    • Author(s)
      1.Kazushi Tamura, Yoshitaka Moriwaki, Tohru Terada, Kentaro Shimizu
    • Organizer
      第60回日本生物物理学会年会
    • Data Source
      KAKENHI-PROJECT-21K12122
  • [Presentation] P-41Trans-AVPGAN: Transformerネットワークを用いた対的生成ネットワークによる抗ウイルスペプチド生成2021

    • Author(s)
      Kano Hasegawa, Yoshitaka Moriwaki, Tohru Terada and Kentaro Shimizu
    • Organizer
      2021年日本バイオインフォマティクス学会年会
    • Data Source
      KAKENHI-PROJECT-21K12122
  • [Presentation] Identifying MoRFs in Disordered Protein Using Enlarged Conserved Features2018

    • Author(s)
      C. Fang, A. Tian, K. Shimizu
    • Organizer
      2018 6th International Conference on Bioinformatics and Computational Biology
    • Int'l Joint Research
    • Data Source
      KAKENHI-PROJECT-17F17050
  • [Presentation] 位置特異的スコアリングマトリックスとサポートベクターマシーンを用いた脂質結合タンパク予測手法の開発2014

    • Author(s)
      植木快、番野雅城、中村周吾、清水謙多郞
    • Organizer
      第14回日本蛋白質科学会年会
    • Place of Presentation
      横浜産貿ホールマリネリア(神奈川県、横浜市)
    • Year and Date
      2014-06-27
    • Data Source
      KAKENHI-PROJECT-23300109
  • [Presentation] PROTEIN-LIGAND BINDING SIMULATIONWITHTHE MARTINI COARSE-GRAINED FORCE FIELD.2014

    • Author(s)
      Tatsuki Negami, Tohru Terada, Kentaro Shimizu
    • Organizer
      Biophysical Society, 58th Annual Meeting
    • Place of Presentation
      サンフランシスコ(アメリカ)
    • Year and Date
      2014-02-18
    • Data Source
      KAKENHI-PROJECT-23300109
  • [Presentation] タンパク質の複合体構造・相互作用に関する総合的な予測・解析/Prediction and analysis of protein complex structures and protein interactions2014

    • Author(s)
      清水謙多郞、寺田透
    • Organizer
      第14回日本蛋白質科学会年会
    • Place of Presentation
      ワークピア横浜(神奈川県、横浜市)
    • Year and Date
      2014-06-25
    • Invited
    • Data Source
      KAKENHI-PROJECT-23300109
  • [Presentation] The factors determining protein-ligand binding processes revealed by comparative coarse-grained simulations2014

    • Author(s)
      Tatsuki Negami, Tohru Terada, Kentaro Shimizu
    • Organizer
      第52回日本生物物理学会年会
    • Place of Presentation
      札幌コンベンションセンター(北海道、札幌市)
    • Year and Date
      2014-09-26
    • Data Source
      KAKENHI-PROJECT-23300109
  • [Presentation] Structural insight into the heme-transfer mechanism between Isd proteins in Staphylococcus aureus2014

    • Author(s)
      Yoshitaka Moriwaki, Tohru Terada, Jose M. M. Caaveiro, Kouhei Tsumoto, Kentaro Shimizu
    • Organizer
      第52回日本生物物理学会年会
    • Place of Presentation
      札幌コンベンションセンター(北海道、札幌市)
    • Year and Date
      2014-09-26
    • Data Source
      KAKENHI-PROJECT-23300109
  • [Presentation] HEME-TRANSFER MECHANISM OF STRUCTURALLY SIMILAR ISD NEAT DOMAINS OF STAPHYLOCOCCUS AUREUS EXHIBITING DIFFERENT AFFINITIES FOR HEME.2014

    • Author(s)
      Yoshitaka Moriwaki, Tohru Terada, Jose M. M. Caaveiro, Yousuke Takaoka, Itaru Hamachi, Kouhei Tsumoto, Kentaro Shimizu
    • Organizer
      Biophysical Society, 58th Annual Meeting
    • Place of Presentation
      サンフランシスコ(アメリカ)
    • Year and Date
      2014-02-19
    • Data Source
      KAKENHI-PROJECT-23300109
  • [Presentation] Effect of basis selection in reconstructing NMR spectra using compressed sensing2014

    • Author(s)
      Kazuya Sumikoshi, Teppei Ikeya, Yutaka Ito, Kentaro Shimizu
    • Organizer
      第52回日本生物物理学会年会
    • Place of Presentation
      札幌コンベンションセンター(北海道、札幌市)
    • Year and Date
      2014-09-25
    • Data Source
      KAKENHI-PROJECT-23300109
  • [Presentation] 黄色ブドウ球菌のヘム輸送蛋白質群Isd system におけるその構造類似性とヘムの不可逆輸送に関する考察2013

    • Author(s)
      Yoshitaka Moriwaki, Tohru Terada, Jose M. M. Caaveiro, Yousuke Takaoka, Itaru Hamachi, Kouhei Tsumoto, Kentaro Shimizu
    • Organizer
      第13回日本蛋白質科学会年会
    • Place of Presentation
      とりぎん文化会館(鳥取県鳥取市)
    • Year and Date
      2013-06-12
    • Data Source
      KAKENHI-PROJECT-23300109
  • [Presentation] 蛋白質立体構造および相互作用の予測2013

    • Author(s)
      清水 謙多郎
    • Organizer
      第4回神経科学と構造生物学の融合研究会
    • Place of Presentation
      岡崎コンファレンスセンター(愛知県岡崎市)
    • Year and Date
      2013-11-19
    • Invited
    • Data Source
      KAKENHI-PROJECT-23300109
  • [Presentation] Development of system that predict sugar binding protein and sugar binding site based on protein sequence using support vector machine.2013

    • Author(s)
      番野 雅城、込山 悠介、中村 周吾、清水 謙多郎
    • Organizer
      日本バイオインフォマティクス学会 2013年年会
    • Place of Presentation
      タワーホール船堀(東京都江戸川区)
    • Year and Date
      2013-10-29
    • Data Source
      KAKENHI-PROJECT-23300109
  • [Presentation] 圧縮センシングを用いたNMRスペクトルの復元法2013

    • Author(s)
      Kazuya Sumikoshi, Teppei Ikeya, Yutaka Ito, Kentaro Shimizu
    • Organizer
      日本生物物理学会 第51回年会
    • Place of Presentation
      国立京都国際会館(京都府京都市)
    • Year and Date
      2013-10-29
    • Data Source
      KAKENHI-PROJECT-23300109
  • [Presentation] 黄色ブドウ球菌のIsd-NEATドメイン間におけるヘム輸送についての考察2013

    • Author(s)
      Yoshitaka Moriwaki, Tohru Terada, Jose M. M. Caaveiro, Yousuke Takaoka, Itaru Hamachi, Kouhei Tsumoto, Kentaro Shimizu
    • Organizer
      日本生物物理学会 第51回年会
    • Place of Presentation
      国立京都国際会館(京都府京都市)
    • Year and Date
      2013-10-30
    • Data Source
      KAKENHI-PROJECT-23300109
  • [Presentation] 代謝型グルタミン酸受容体の活性化過程の動的モデルの構築2013

    • Author(s)
      冨士原 海太、根上 樹、寺田 透、清水 謙多郎
    • Organizer
      日本生物物理学会 第51回年会
    • Place of Presentation
      国立京都国際会館(京都府京都市)
    • Year and Date
      2013-10-30
    • Data Source
      KAKENHI-PROJECT-23300109
  • [Presentation] UTProt: Database Integration and Tool Development for Interactomics Utilizing Biosemantics2013

    • Author(s)
      込山 悠介、番野 雅城、Gul Saad、遣水 優行、植木 快、清水 謙多郎
    • Organizer
      日本バイオインフォマティクス学会 2013年年会
    • Place of Presentation
      タワーホール船堀(東京都江戸川区)
    • Year and Date
      2013-10-29
    • Data Source
      KAKENHI-PROJECT-23300109
  • [Presentation] MARTINI粗視化力場を用いたタンパク質-リガンド結合過程の比較シュミレーション2013

    • Author(s)
      根上 樹、寺田 透、清水 謙多郎
    • Organizer
      日本生物物理学会 第51回年会
    • Place of Presentation
      国立京都国際会館(京都府京都市)
    • Year and Date
      2013-10-29
    • Data Source
      KAKENHI-PROJECT-23300109
  • [Presentation] Sequence derived predictor of lipid-binding proteins with support vector machine2013

    • Author(s)
      植木 快、込山 悠介、番野 雅城、中村 周吾、清水 謙多郎
    • Organizer
      日本バイオインフォマティクス学会 2013年年会
    • Place of Presentation
      タワーホール船堀(東京都江戸川区)
    • Year and Date
      2013-10-29
    • Data Source
      KAKENHI-PROJECT-23300109
  • [Presentation] Carbohydrate-binding proteins : A sequence-based prediction model and the database development2010

    • Author(s)
      W.Cao, S.Someya, M.Kakuta, K.Sumikoshi, S.Nakamura, T.Terada, K. K. K.Shimizu
    • Organizer
      The 2010 Annual Conference of the Japanese Society for Bioinformatics (JSBi2010)
    • Place of Presentation
      九州大学(福岡)
    • Data Source
      KAKENHI-PROJECT-20500269
  • [Presentation] タンパク質-タンパク質ドッキングへの分子内フレキシビリティの導入2010

    • Author(s)
      角越和也,中村周吾,清水謙多郎
    • Organizer
      日本生物物理学会第48回年会
    • Place of Presentation
      東北大学(宮城)
    • Data Source
      KAKENHI-PROJECT-20500269
  • [Presentation] 二次構造情報を取り入れた分子動力学法によるタンパク質立体構造予測法の一般性の検証2010

    • Author(s)
      寺田透,西村麻彦,清水謙多郎
    • Organizer
      日本生物物理学会第48回年会
    • Place of Presentation
      東北大学(宮城)
    • Data Source
      KAKENHI-PROJECT-20500269
  • [Presentation] バイオロジカルユニットを考慮したリガンド結合タンパク質データベースの構築2009

    • Author(s)
      池澤弘貴,森田瑞樹,清水謙多郎
    • Organizer
      日本生物物理学会第47回年会
    • Place of Presentation
      徳島文理大学(徳島)
    • Data Source
      KAKENHI-PROJECT-20500269
  • [Presentation] all-βタンパク質の二次構造拘束付きマルチカノニカル分子動力学シミュレーション2009

    • Author(s)
      西村麻彦,寺田透,清水謙多郎
    • Organizer
      日本生物物理学会第47回年会
    • Place of Presentation
      徳島文理大学(徳島)
    • Data Source
      KAKENHI-PROJECT-20500269
  • [Presentation] BLASTと機械学習を用いたアミノ酸配列からのレクチン様タンパク質の予測2008

    • Author(s)
      染谷星志, 角田将典, 森田瑞樹, 角越和也, 中村周吾, 清水謙多郎
    • Organizer
      第31回日本分子生物学会年会
    • Place of Presentation
      神戸
    • Year and Date
      2008-12-12
    • Data Source
      KAKENHI-PROJECT-20016006
  • [Presentation] 精密化プロセスを含めたタンパク質-タンパク質ドッキング手法の開発2008

    • Author(s)
      角越和也,寺田透,中村周吾,清水謙多郎
    • Organizer
      日本生物物理学会第46回年会
    • Place of Presentation
      福岡国際会議場(福岡)
    • Data Source
      KAKENHI-PROJECT-20500269
  • [Presentation] タンパク質ペアに対するカーネル関数を用いたタンパク質間相互作用予測2008

    • Author(s)
      角田将典,角越和也,中村周吾,清水謙多郎
    • Organizer
      第8回日本蛋白質科学会年会
    • Place of Presentation
      タワーホール船堀(東京)
    • Data Source
      KAKENHI-PROJECT-20500269
  • [Presentation] タンパク質のオーダー・ディスオーダーループの配列構造相関の解析2008

    • Author(s)
      中村周吾,清水謙多郎
    • Organizer
      第8回日本蛋白質科学会年会
    • Place of Presentation
      タワーホール船堀(東京)
    • Data Source
      KAKENHI-PROJECT-20500269
  • [Presentation] 生体分子の溶媒効果:マルチカノニカルQM/MM-MDによる研究2008

    • Author(s)
      城野亮太,渡邊佑輔,清水謙多郎,寺田透
    • Organizer
      日本生物物理学会第46回年会
    • Place of Presentation
      福岡
    • Year and Date
      2008-12-05
    • Data Source
      KAKENHI-PROJECT-20500269
  • [Presentation] 分子動力学シミュレーションによるWWドメインのフォールディング機構の解析2008

    • Author(s)
      西村麻彦,西謙一郎,寺田透,清水謙多郎
    • Organizer
      第8回日本蛋白質科学会年会
    • Place of Presentation
      タワーホール船堀(東京)
    • Data Source
      KAKENHI-PROJECT-20500269
  • [Presentation] 生体分子の溶媒効果:マルチカノニカルQM/MM-MDによる研究2008

    • Author(s)
      城野亮太,渡邊佑輔,清水謙多郎,寺田透
    • Organizer
      日本生物物理学会第46回年会
    • Place of Presentation
      福岡国際会議場(福岡)
    • Data Source
      KAKENHI-PROJECT-20500269
  • [Presentation] タンパク質構造予測2008

    • Author(s)
      清水謙多郎
    • Organizer
      JSTゲノムリテラシー講座
    • Place of Presentation
      JSTサイエンスプラザ(東京)
    • Data Source
      KAKENHI-PROJECT-20500269
  • [Presentation] ドメイン配列を用いたタンパク質間相互作用予測2008

    • Author(s)
      角田将典,角越和也,中村周吾,清水謙多郎
    • Organizer
      日本生物物理学会第46回年会
    • Place of Presentation
      福岡国際会議場(福岡)
    • Data Source
      KAKENHI-PROJECT-20500269
  • [Presentation] Sequence-structure correlation analysis for protein loop regions2007

    • Author(s)
      Shugo Nakamura, Mizuki Morita, Masanori Kakuta, Kentaro Shimizu
    • Organizer
      Forty-Fifth Annual Meeting of the Biophysical Society of Japan, 2P004
    • Place of Presentation
      Yokohama
    • Year and Date
      2007-12-22
    • Description
      「研究成果報告書概要(欧文)」より
    • Data Source
      KAKENHI-PROJECT-17500191
  • [Presentation] Protein-protein docking simulations2006

    • Author(s)
      Kentaro Shimizu
    • Organizer
      Symposium of Institute for Protein Research, Osaka University
    • Place of Presentation
      Osaka
    • Year and Date
      2006-03-23
    • Description
      「研究成果報告書概要(欧文)」より
    • Data Source
      KAKENHI-PROJECT-17500191
  • [Presentation] 蛋白質複合体のドッキングシミュレーション2006

    • Author(s)
      清水謙多郎
    • Organizer
      大阪大学蛋白質研究所セミナー「生体分子構造情報の時間軸への展開による生命機能の解読」
    • Place of Presentation
      大阪
    • Year and Date
      2006-03-23
    • Description
      「研究成果報告書概要(和文)」より
    • Data Source
      KAKENHI-PROJECT-17500191
  • [Presentation] Protein tertiary structure prediction based on contact number prediction2006

    • Author(s)
      Takashi Ishida, Shugo Nakamura, Kentaro Shimizu
    • Organizer
      Fifth East Asian Biophysics Symposium & Forty-Fourth Annual Meeting of the Biophysical Society of Japan
    • Place of Presentation
      Okinawa
    • Year and Date
      2006-11-14
    • Description
      「研究成果報告書概要(欧文)」より
    • Data Source
      KAKENHI-PROJECT-17500191
  • [Presentation] Improving efficiency of conformation sampling in multicanonical molecular dynamics simulation2006

    • Author(s)
      Tohru Terada, Kentaro Shimizu
    • Organizer
      Fifth East Asian Biophysics Symposium & Forty-Fourth Annual Meeting of the Biophysical Society of Japan, 46, 1P581
    • Place of Presentation
      Okinawa
    • Year and Date
      2006-11-13
    • Description
      「研究成果報告書概要(欧文)」より
    • Data Source
      KAKENHI-PROJECT-17500191
  • [Presentation] Folding simulation of the B-domain of staphylococcal protein A2006

    • Author(s)
      Ken-ichiro Nishi, Tohru Terada, Kentaro Shimizu
    • Organizer
      Fifth East Asian Biophysics Symposium & Forty-Fourth Annual Meeting of the Biophysical Society of Japan, 46, 1P573
    • Place of Presentation
      Okinawa
    • Year and Date
      2006-11-13
    • Description
      「研究成果報告書概要(欧文)」より
    • Data Source
      KAKENHI-PROJECT-17500191
  • [Presentation] Protein structure refinement by using multicanonical molecular dynamics simulation2005

    • Author(s)
      Ryuichiro Ishitani, Tohru Terada, Shugo Nakamura, Kentaro Shimizu
    • Organizer
      Forty-Third Annual Meeting of the Biophysical Society of Japan, 1P008
    • Place of Presentation
      Sapporo
    • Year and Date
      2005-11-23
    • Description
      「研究成果報告書概要(欧文)」より
    • Data Source
      KAKENHI-PROJECT-17500191
  • 1.  NAKAMURA Shugo (90272442)
    # of Collaborated Projects: 17 results
    # of Collaborated Products: 26 results
  • 2.  TERADA Tohru (40359641)
    # of Collaborated Projects: 7 results
    # of Collaborated Products: 23 results
  • 3.  SUMIKOSHI Kazuya (90431832)
    # of Collaborated Projects: 3 results
    # of Collaborated Products: 4 results
  • 4.  池口 満徳 (60261955)
    # of Collaborated Projects: 3 results
    # of Collaborated Products: 0 results
  • 5.  伊藤 素行 (20377906)
    # of Collaborated Projects: 2 results
    # of Collaborated Products: 0 results
  • 6.  KAMEDA Hisao (10011660)
    # of Collaborated Projects: 1 results
    # of Collaborated Products: 0 results
  • 7.  KAKUDA Hiroyasu (70152600)
    # of Collaborated Projects: 1 results
    # of Collaborated Products: 0 results
  • 8.  TERASHIMA Motoaki (20114928)
    # of Collaborated Projects: 1 results
    # of Collaborated Products: 0 results
  • 9.  KASAI Takumi (70027382)
    # of Collaborated Projects: 1 results
    # of Collaborated Products: 0 results
  • 10.  ASHIHARA Hyo (00242347)
    # of Collaborated Projects: 1 results
    # of Collaborated Products: 0 results
  • 11.  Shuichi Fukuyoshi (10456410)
    # of Collaborated Projects: 1 results
    # of Collaborated Products: 0 results
  • 12.  砂原 秀樹 (20206577)
    # of Collaborated Projects: 1 results
    # of Collaborated Products: 0 results
  • 13.  青柳 龍也 (40202494)
    # of Collaborated Projects: 1 results
    # of Collaborated Products: 0 results
  • 14.  中山 泰一 (70251709)
    # of Collaborated Projects: 1 results
    # of Collaborated Products: 0 results
  • 15.  高橋 広夫 (30454367)
    # of Collaborated Projects: 1 results
    # of Collaborated Products: 0 results
  • 16.  佐々木 博己 (60235265)
    # of Collaborated Projects: 1 results
    # of Collaborated Products: 0 results
  • 17.  田胡 和哉
    # of Collaborated Projects: 1 results
    # of Collaborated Products: 0 results
  • 18.  張 勇兵
    # of Collaborated Projects: 1 results
    # of Collaborated Products: 0 results
  • 19.  FANG CHUN
    # of Collaborated Projects: 1 results
    # of Collaborated Products: 9 results
  • 20.  KADOTA Koji
    # of Collaborated Projects: 0 results
    # of Collaborated Products: 2 results
  • 21.  西山 智明
    # of Collaborated Projects: 0 results
    # of Collaborated Products: 1 results

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