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Theoretical investigation of reaction fields of biological macromolecular systems based on quantum sciences and mathematical informatics

Research Project

Project/Area Number 25287099
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypePartial Multi-year Fund
Section一般
Research Field Mathematical physics/Fundamental condensed matter physics
Research InstitutionUniversity of Hyogo

Principal Investigator

Tateno Masaru  兵庫県立大学, 生命理学研究科, 教授 (40291926)

Co-Investigator(Kenkyū-buntansha) 山崎 和彦  国立研究開発法人産業技術総合研究所, その他部局等, 研究員 (00358243)
筒井 公子  岡山大学, 医歯(薬)学総合研究科, 名誉教授 (70144748)
Co-Investigator(Renkei-kenkyūsha) KINO HIORI  独立行政法人物質・材料研究機構, 計算科学センター, 主任研究員 (70282605)
Project Period (FY) 2013-04-01 – 2017-03-31
Project Status Completed (Fiscal Year 2016)
Budget Amount *help
¥19,110,000 (Direct Cost: ¥14,700,000、Indirect Cost: ¥4,410,000)
Fiscal Year 2015: ¥6,110,000 (Direct Cost: ¥4,700,000、Indirect Cost: ¥1,410,000)
Fiscal Year 2014: ¥6,110,000 (Direct Cost: ¥4,700,000、Indirect Cost: ¥1,410,000)
Fiscal Year 2013: ¥6,890,000 (Direct Cost: ¥5,300,000、Indirect Cost: ¥1,590,000)
Keywords電子ダイナミクス / ハイブリッド触媒 / 電子状態理論 / パターン認識 / 情報微分幾何学 / ゲノムDNA / リボザイム / 転写制御 / 電子構造理論 / 情報理論 / 機械学習 / 情報幾何学 / ゲノム情報学 / 多様体 / 計算科学 / 情報科学 / 量子科学 / 生命物理学 / 生体高分子 / DNA / タンパク質 / 核酸 / 生体触媒反応における電子構造のダイナミクス / ゲノムDNAの高次構造モデル / 転写制御配列の自動同定システム / 自動解析ウェブサービスシステム / 細胞内情報伝達の生体反応 / GTP加水分解反応メカニズム / 結晶構造のリファインメント解析技術 / 情報科学・計算科学の融合
Outline of Final Research Achievements

By systematically combining quantum science and mathematical informatics, we obtained the following achievements: i) To precisely identify even weak and subtle signals that act as functional sequence motifs in genome DNA, novel algorithms were developed together with mathematical descriptions based on an information geometrical manifold, and applied to reveal the motifs recognized by DNA topoisomerase (topo) IIb. ii) Mechanisms to recognize the identified motifs were also analyzed in combination with structural modeling of the DNA-topoIIb complex and hybrid ab initio quantum mechanics (QM) molecular dynamics (MD) simulations of the complex. The informatics and QM analyses showed that the catalysis acts in concert with the DNA recognition by topoIIb. iii) In some biological systems, the catalytic mechanisms that could uniquely be characteristic to organisms were revealed by using hybrid MD simulations, and dynamical processes of the electronic structure rearrangements were elucidated.

Report

(5 results)
  • 2016 Annual Research Report   Final Research Report ( PDF )
  • 2015 Annual Research Report
  • 2014 Annual Research Report
  • 2013 Annual Research Report
  • Research Products

    (146 results)

All 2017 2016 2015 2014 2013 Other

All Int'l Joint Research (2 results) Journal Article (9 results) (of which Int'l Joint Research: 1 results,  Peer Reviewed: 9 results,  Open Access: 7 results,  Acknowledgement Compliant: 5 results) Presentation (133 results) (of which Int'l Joint Research: 35 results,  Invited: 8 results) Remarks (2 results)

  • [Int'l Joint Research] Institut de Biologie Structurale(France)

    • Related Report
      2016 Annual Research Report
  • [Int'l Joint Research] 構造生物学研究所(グルノーブル)(フランス)

    • Related Report
      2015 Annual Research Report
  • [Journal Article] Novel Strategy for Discrimination of Transcription Factor Binding Motif Employing Mathematical Neural Network2017

    • Author(s)
      Asuka Sugimoto, Takuya Sumi, Jiyoung Kang, and Masaru Tateno
    • Journal Title

      J. Phys. Soc. Jpn.

      Volume: 印刷中

    • NAID

      210000134453

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Effects of a Positive Feedback Loop upon the Stability of Bi-connected Elementary Biochemical Reaction Cycle2017

    • Author(s)
      Jiyoung kang, and Masaru Tateno
    • Journal Title

      J. Phys. Soc. Jpn.

      Volume: 印刷中

    • NAID

      40021254431

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Electronic Structure Rearrangements in Hybrid Ribozyme/Protein Catalysis2017

    • Author(s)
      Jiyoung Kang, Hiori Kino, Martin J. Field, and Masaru Tateno
    • Journal Title

      J. Phys. Soc. Jpn.

      Volume: 86 Issue: 4 Pages: 044801-044801

    • DOI

      10.7566/jpsj.86.044801

    • NAID

      210000134350

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] Simulated Annealing-Extended Sampling for Multicomponent Decomposition of Spectral Data of DNA Complexed with Peptide2017

    • Author(s)
      Jiyoung Kang, Kazuhiko Yamasaki, Kuniaki Sano, Ken Tsutsui, Kimiko M. Tsutsui, and Masaru Tateno
    • Journal Title

      J. Phys. Soc. Jpn.

      Volume: 86 Issue: 1 Pages: 014802-014802

    • DOI

      10.7566/jpsj.86.014802

    • NAID

      40021057753

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Complex structure of cytochrome c-cytochrome c oxidase reveals a novel protein-protein interaction mode2017

    • Author(s)
      Satoru Shimada, Kyoko Shinzawa‐Itoh, Junpei Baba, Shimpei Aoe, Atsuhiro Shimada, Eiki Yamashita, Jiyoung Kang, Masaru Tateno, Shinya Yoshikawa, and Tomitake Tsukihara
    • Journal Title

      EMBO J.

      Volume: 86 Issue: 3 Pages: 291-300

    • DOI

      10.15252/embj.201695021

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] The combination of sequence-specific and nonspecific binding modes of transcription factor SATB12016

    • Author(s)
      Kazuhiko Yamasaki and Tomoko Yamasaki
    • Journal Title

      Biochemical Journal

      Volume: 473 Issue: 19 Pages: 3321-3339

    • DOI

      10.1042/bcj20160236

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Genomic regions targeted by DNA topoisomerase II frequently interact with a nuclear scafforld/matrix protein hnRNP U/SAF-A/SP1202015

    • Author(s)
      Miyaji, M., Furuta, R., Sano, K., Tsutsui, K. M. and Tsutsui, K.
    • Journal Title

      J. Cell. Biochem.

      Volume: 116 Issue: 4 Pages: 667-85

    • DOI

      10.1002/jcb.25024

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Nuclear dynamics of topoisomerase IIβ reflects its catalytic activity that is regulated by binding of RNA to the C-terminal domain.2014

    • Author(s)
      Onoda A, Hosoya O, Sano K, Kiyama K, Kimura H, Kawano S, Furuta R, Miyaji M, Tsutsui K, Tsutsui KM.
    • Journal Title

      Nucleic Acids Res

      Volume: 42 Issue: 14 Pages: 9005-9020

    • DOI

      10.1093/nar/gku640

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] The CENP-O complex requirement varies among different cell types.2014

    • Author(s)
      Kagawa, N., Hori, T., Hoki, Y., Hosoya, O., Tsutsui, K., Saga, Y., Sado, T., and *Fukagawa, T.
    • Journal Title

      Chrom. Research

      Volume: in press Issue: 3 Pages: 293-303

    • DOI

      10.1007/s10577-014-9404-1

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed / Open Access
  • [Presentation] Structural and thermodynamic mechanisms of selectivity and cooperativity in recognition of supercoiled DNA-recognition (SDR) peptide and crossover DNA2017

    • Author(s)
      Hiroshi Nishigami, Jiyoung Kang, Kakeru Sakabe, Kuniaki Sano, Kimiko M. Tsutsui, Ken Tsutsui, Kazuhiko Yamasaki, Masaru Tateno
    • Organizer
      2016 Leading Program Evaluation Conference
    • Place of Presentation
      Center for Advanced Science and Technology Hyogo (CAST)
    • Year and Date
      2017-03-13
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Applicability augmented by extending of sampling space in molecular docking simulation for drug design2017

    • Author(s)
      Takuya Sumi, Jiyoung Kang, Ryuichiro Terada, Hiroshi Yamaguchi, and Masaru Tateno
    • Organizer
      2016 Leading Program Evaluation Conference
    • Place of Presentation
      Center for Advanced Science and Technology Hyogo (CAST)
    • Year and Date
      2017-03-13
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Development of novel strategy for discrimination of transcription factor binding motifs (TFBMs) employing mathematical neural network2017

    • Author(s)
      Masaru Tateno, Asuka Sugimoto, Takuya Sumi, Kakeru Sakabe, and Jiyoung Kang
    • Organizer
      2016 Leading Program Evaluation Conference
    • Place of Presentation
      Center for Advanced Science and Technology Hyogo (CAST)
    • Year and Date
      2017-03-13
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Genome-wide identification of broad-range diverse sequence motifs of topoisomerase IIβ operating sites2017

    • Author(s)
      Asuka Sugimoto, Jiyoung Kang, Kakeru Sakabe, Takuya Sumi, and Masaru Tateno
    • Organizer
      2016 Leading Program Evaluation Conference
    • Place of Presentation
      Center for Advanced Science and Technology Hyogo (CAST)
    • Year and Date
      2017-03-13
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Theoretical analysis of dynamical mechanisms of ligand recognition by cytochrome c oxidase2017

    • Author(s)
      Ryuichiro Terada, Jiyoung Kang, Kakeru Sakabe, and Masaru Tateno
    • Organizer
      2016 Leading Program Evaluation Conference
    • Place of Presentation
      Center for Advanced Science and Technology Hyogo (CAST)
    • Year and Date
      2017-03-13
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Theoretical study of editing reaction mechanism by the complex of valyl-tRNA synthetase and the mis-aminoacylated tRNAVal2017

    • Author(s)
      Kakeru Sakabe, Jiyoung Kang, and Masaru Tateno
    • Organizer
      2016 Leading Program Evaluation Conference
    • Place of Presentation
      Center for Advanced Science and Technology Hyogo (CAST)
    • Year and Date
      2017-03-13
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Dynamical rearrangements of electronic structure in editing reaction by hybrid ribozyme/protein catalyst2017

    • Author(s)
      Jiyoung Kang and Masaru Tateno
    • Organizer
      2016 Leading Program Evaluation Conference
    • Place of Presentation
      Center for Advanced Science and Technology Hyogo (CAST)
    • Year and Date
      2017-03-13
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Electronic structure analysis of O2-tolerance mechanisms of hydrogenase by hybrid ab initio quantum mechanics/molecular mechanics simulation2017

    • Author(s)
      Jaehyun Kim, Jiyoung Kang, and Masaru Tateno
    • Organizer
      2016 Leading Program Evaluation Conference
    • Place of Presentation
      Center for Advanced Science and Technology Hyogo (CAST)
    • Year and Date
      2017-03-13
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Dynamical mechanisms of structural transitions acting as functional switch induced by the ligand binding in cytochrome c oxidase2016

    • Author(s)
      Ryuichiro Terada, Jiyoung Kang, and Masaru Tateno
    • Organizer
      The 39th Annual Meeting of The Molecular Biology Society of Japan
    • Place of Presentation
      Pacifico Yokohama
    • Year and Date
      2016-11-30
    • Related Report
      2016 Annual Research Report
  • [Presentation] Structural modeling of initial ES complex of topoisomerase IIB and target DNA employing molecular dynamics simulation2016

    • Author(s)
      Kakeru Sakabe, Hiroshi Nishigami, Jiyoung Kang, and Masaru Tateno
    • Organizer
      The 39th Annual Meeting of The Molecular Biology Society of Japan
    • Place of Presentation
      Pacifico Yokohama
    • Year and Date
      2016-11-30
    • Related Report
      2016 Annual Research Report
  • [Presentation] Extended applicability of molecular docking simulation for ligand design by optimizing configurational and conformational sampling spaces2016

    • Author(s)
      Takuya Sumi, Hiroshi Yamaguchi, Ryuichiro Terada, Jiyoung Kang, and Masaru Tateno
    • Organizer
      The 39th Annual Meeting of The Molecular Biology Society of Japan
    • Place of Presentation
      Pacifico Yokohama
    • Year and Date
      2016-11-30
    • Related Report
      2016 Annual Research Report
  • [Presentation] Molecular dynamics docking simulation to elucidate selective binding mechanisms of supercoiled-DNA recognition (SDR) peptide and spatially-crossover DNA2016

    • Author(s)
      Hiroshi Nishigami, Kakeru Sakabe, Jiyoung Kang, Kuniaki Sano, Kimiko Tsutsui, Ken Tsutsui, Kazuhiko Yamasaki, and Masaru Tateno
    • Organizer
      The 39th Annual Meeting of The Molecular Biology Society of Japan
    • Place of Presentation
      Pacifico Yokohama
    • Year and Date
      2016-11-30
    • Related Report
      2016 Annual Research Report
  • [Presentation] Hybrid ab initio molecular dynamical simulation of cytochrome c oxidase: Mechanisms of structural changes by dynamical ligand recognition2016

    • Author(s)
      Ryuichiro Terada, Jiyoung Kang, and Masaru Tateno
    • Organizer
      The 54th Annual Meeting of the Biophysical Society of Japan
    • Place of Presentation
      Tsukuba International Congress Center
    • Year and Date
      2016-11-25
    • Related Report
      2016 Annual Research Report
  • [Presentation] Hydrogenase : ab initio quantum mechanics study of oxygen-tolerance mechanism2016

    • Author(s)
      Jaehyun Kim, Jiyoung Kang, and Masaru Tateno
    • Organizer
      The 54th Annual Meeting of the Biophysical Society of Japan
    • Place of Presentation
      Tsukuba International Congress Center
    • Year and Date
      2016-11-25
    • Related Report
      2016 Annual Research Report
  • [Presentation] Identification of optimal parameter values in ligand-receptor docking calculation to extend applicability2016

    • Author(s)
      Takuya Sumi, Hiroshi Yamaguchi, Ryuichiro Terada, Jiyoung Kang, and Masaru Tateno
    • Organizer
      The 54th Annual Meeting of the Biophysical Society of Japan
    • Place of Presentation
      Tsukuba International Congress Center
    • Year and Date
      2016-11-25
    • Related Report
      2016 Annual Research Report
  • [Presentation] Complex structure of cytochrome c and cytochrome c oxidase shows a novel inter-protein interaction mode2016

    • Author(s)
      Satoru Shimada, Kyoko Shinzawa-Itoh, Junpei Baba, Shimpei Aoe, Atsuhiro Shimada, Eiki Yamashita, Jiyoung Kang, Masaru Tateno, Shinya Yoshikawa, and Tomitake Tsukihara
    • Organizer
      The 54th Annual Meeting of the Biophysical Society of Japan
    • Place of Presentation
      Tsukuba International Congress Center
    • Year and Date
      2016-11-25
    • Related Report
      2016 Annual Research Report
  • [Presentation] Identification of initial ES complex of topoisomerase IIβ and target DNA employing molecular dynamics docking simulation2016

    • Author(s)
      Kakeru Sakabe, Hiroshi Nisihigami, Jiyoung Kang, Masaru Tateno
    • Organizer
      The 54th Annual Meeting of the Biophysical Society of Japan
    • Place of Presentation
      Tsukuba International Congress Center
    • Year and Date
      2016-11-25
    • Related Report
      2016 Annual Research Report
  • [Presentation] Molecular dynamics docking study on selective binding mechanisms of supercoiled-DNA recognition (SDR) peptide and spatially-crossover DNA2016

    • Author(s)
      Hiroshi Nishigami, Kakeru Sakabe, Jiyoung Kang, Kuniaki Sano, Kimiko Tsutsui, Ken Tsutsui, Kazuhiko Yamasaki, and Masaru Tateno
    • Organizer
      The 54th Annual Meeting of the Biophysical Society of Japan
    • Place of Presentation
      Tsukuba International Congress Center
    • Year and Date
      2016-11-25
    • Related Report
      2016 Annual Research Report
  • [Presentation] Enhancement of sampling space in multivariate analysis of experimental big data in various biological sciences2016

    • Author(s)
      Jiyoung Kang, Kazuhiko Yamasaki, and Masaru Tateno
    • Organizer
      The 54th Annual Meeting of the Biophysical Society of Japan
    • Place of Presentation
      Tsukuba International Congress Center
    • Year and Date
      2016-11-25
    • Related Report
      2016 Annual Research Report
  • [Presentation] Development and Application of Algorithms to Identify Functionally-Clustered Genes in Eukaryotic Genomes2016

    • Author(s)
      Kakeru Sakabe, Jiyoung Kang, and Masaru Tateno
    • Organizer
      5th Informatics in Biology Medicine and Pharmacology
    • Place of Presentation
      東京国際交流館プラザ平成(東京お台場)
    • Year and Date
      2016-09-29
    • Related Report
      2016 Annual Research Report
  • [Presentation] Broad-range applicability of molecular docking calculation of ligand and receptor by optimizing configurational and conformational sampling spaces2016

    • Author(s)
      Takuya Sumi, Hiroshi Yamaguchi, Ryuichiro Terada, Jiyoung Kang, and Masaru Tateno
    • Organizer
      5th Informatics in Biology Medicine and Pharmacology
    • Place of Presentation
      東京国際交流館プラザ平成(東京お台場)
    • Year and Date
      2016-09-29
    • Related Report
      2016 Annual Research Report
  • [Presentation] Enhancement of spectral curve sampling in multivariate analysis of experimental big data of various biological sciences2016

    • Author(s)
      Jiyoung Kang and Masaru Tateno
    • Organizer
      5th Informatics in Biology Medicine and Pharmacology
    • Place of Presentation
      東京国際交流館プラザ平成(東京お台場)
    • Year and Date
      2016-09-29
    • Related Report
      2016 Annual Research Report
  • [Presentation] Structure of complex of cytochrome c and cytochrome c oxidase shows the novel protein-protein interaction style2016

    • Author(s)
      Satoru Shimada, Shinpei Aoe, Kyoko Shinzawa-Itoh, Jumpei Baba, Atsuhiro Shimada, Jiyoung Kang, Masaru Tateno, Eiki Yamashita, Shinya Yoshikawa, and Tomitake Tsukihara
    • Organizer
      The 16th Annual Meeting of the Protein Science Society of Japan
    • Place of Presentation
      Fukuoka International Congress Center
    • Year and Date
      2016-07-07
    • Related Report
      2016 Annual Research Report
  • [Presentation] Novel extended sampling method for multivariate analysis calculation of experimental big data in biochemistry and bioinformatics2016

    • Author(s)
      Jiyoung Kang, Kazuhiko Yamasaki, and Masaru Tateno
    • Organizer
      The 16th Annual Meeting of the Protein Science Society of Japan
    • Place of Presentation
      Fukuoka International Congress Center
    • Year and Date
      2016-07-07
    • Related Report
      2016 Annual Research Report
  • [Presentation] Hybrid ab initio QM/MM molecular dynamics study of catalytic reaction of cytidine deaminase2016

    • Author(s)
      Masaru Tateno, Jiyoung Kang, Takashi Taniguchi, and Kakeru Sakabe
    • Organizer
      The 16th Annual Meeting of the Protein Science Society of Japan
    • Place of Presentation
      Fukuoka International Congress Center
    • Year and Date
      2016-07-07
    • Related Report
      2016 Annual Research Report
  • [Presentation] Hybrid ab initio quantum mechanics analysis of O2-binding to the CuB-Fea3 binuclear center of cytochrome c oxidase2016

    • Author(s)
      Ryuichiro Terada, Jiyoung Kang, and Masaru Tateno
    • Organizer
      The 16th Annual Meeting of the Protein Science Society of Japan
    • Place of Presentation
      Fukuoka International Congress Center
    • Year and Date
      2016-07-07
    • Related Report
      2016 Annual Research Report
  • [Presentation] ab initio electronic structure calculation of proximal cluster in membrane bound hydrogenases (MBH)2016

    • Author(s)
      Jaehyun Kim、Jiyoung Kang, and Masaru Tateno
    • Organizer
      The 16th Annual Meeting of the Protein Science Society of Japan
    • Place of Presentation
      Fukuoka International Congress Center
    • Year and Date
      2016-07-07
    • Related Report
      2016 Annual Research Report
  • [Presentation] Proton transfer mechanisms in photosystem II : hybrid ab inito quantum mechanics study2016

    • Author(s)
      Atsushi Nakamura, Jiyoung Kang, Yasufumi Umena, Keisuke Kawakami, Jian-Ren Shen, Nobuo Kamiya, and Masaru Tateno
    • Organizer
      The 16th Annual Meeting of the Protein Science Society of Japan
    • Place of Presentation
      Fukuoka International Congress Center
    • Year and Date
      2016-07-07
    • Related Report
      2016 Annual Research Report
  • [Presentation] Theoretical Analysis of Dynamical Mechanisms of Ligand-recognition by Cytochrome c Oxidase Employing Hybrid ab initio Quantum Mechanics/Molecular Mechanics Molecular Dynamics Simulation2016

    • Author(s)
      Jiyoung Kang, Ryuichiro Terada, Masaru Tateno
    • Organizer
      BIT’s 7th Annual Global Congress of Catalysis-2016
    • Place of Presentation
      KINTEX, Goyang, Korea
    • Year and Date
      2016-06-30
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Functional Mechanisms of Biological Macromolecular Systems Revealed by Hybrid ab initio Quantum Mechanics Molecular Dynamics2016

    • Author(s)
      Masaru Tateno
    • Organizer
      BIT’s 7th Annual Global Congress of Catalysis-2016
    • Place of Presentation
      KINTEX, Goyang, Korea
    • Year and Date
      2016-06-30
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Investigation of Oxygen Tolerance Mechanism of Membrane-bound Hydrogenase with use of ab initio Electronic Structure Calculation2016

    • Author(s)
      Jaehyun Kim, Jiyoung Kang, Masaru Tateno
    • Organizer
      BIT’s 7th Annual Global Congress of Catalysis-2016
    • Place of Presentation
      KINTEX, Goyang, Korea
    • Year and Date
      2016-06-30
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Stability of Bi-Connected Elementary Reaction Loop (bc-ERL) Involving Positive Feed-Back Loop2016

    • Author(s)
      Jiyoung Kang, Masaru Tateno
    • Organizer
      International School and Conference on Networks Science, NetSci 2016,
    • Place of Presentation
      Seoul, Korea
    • Year and Date
      2016-05-30
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Theoretical investigation of electronic structure of frontier orbitals of proximal cluster responsible for electron transfer from catalytic center to proximal cluster in membrane-bound hydrogenase (MBH) (oral)2016

    • Author(s)
      Jaehyun Kim, Jiyoung Kang, Masaru Tateno
    • Organizer
      The 3rd Annual Evaluation Conference of the Leading Program, University of Hyogo for the school year of 2015
    • Place of Presentation
      先端科学技術センター(兵庫県赤穂郡)
    • Year and Date
      2016-03-14
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Computational study of solvated structure of the complex of valyl-tRNA synthetase (ValRS) and the mis-aminoacylated tRNAVal (oral)2016

    • Author(s)
      Kakeru Sakabe, Jiyoung Kang, Masaru Tateno
    • Organizer
      The 3rd Annual Evaluation Conference of the Leading Program, University of Hyogo for the school year of 2015
    • Place of Presentation
      先端科学技術センター(兵庫県赤穂郡)
    • Year and Date
      2016-03-14
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Theoretical investigation of electronic structure of frontier orbitals of proximal cluster responsible for electron transfer from catalytic center to proximal cluster in membrane-bound hydrogenase (MBH) (poster)2016

    • Author(s)
      Jaehyun Kim, Jiyoung Kang, Masaru Tateno
    • Organizer
      The 3rd Annual Evaluation Conference of the Leading Program, University of Hyogo for the school year of 2015
    • Place of Presentation
      先端科学技術センター(兵庫県赤穂郡)
    • Year and Date
      2016-03-14
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Computational study of solvated structure of the complex of valyl-tRNA synthetase (ValRS) and the mis-aminoacylated tRNAVal (poster)2016

    • Author(s)
      Kakeru Sakabe, Jiyoung Kang, Masaru Tateno
    • Organizer
      The 3rd Annual Evaluation Conference of the Leading Program, University of Hyogo for the school year of 2015
    • Place of Presentation
      先端科学技術センター(兵庫県赤穂郡)
    • Year and Date
      2016-03-14
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Theoretical analysis of catalytic reaction mechanism in cytidine deaminase that is responsible for RNA editing2016

    • Author(s)
      Takashi Taniguchi, Jiyoung Kang, Masaru Tateno
    • Organizer
      The 3rd Annual Evaluation Conference of the Leading Program, University of Hyogo for the school year of 2015
    • Place of Presentation
      先端科学技術センター(兵庫県赤穂郡)
    • Year and Date
      2016-03-14
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Hybrid ab initio quantum mechanics/molecular mechanics simulation of ligand binding to Cu-Fe binuclear center of cytochrome c oxidase2016

    • Author(s)
      Ryuichiro Terada, Jiyoung Kang, Masaru Tateno
    • Organizer
      The 3rd Annual Evaluation Conference of the Leading Program, University of Hyogo for the school year of 2015
    • Place of Presentation
      先端科学技術センター(兵庫県赤穂郡)
    • Year and Date
      2016-03-14
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Computational docking study of glutamate transporter and drugs2016

    • Author(s)
      Takuya Sumi, Jiyoung Kang, Masaru Tateno
    • Organizer
      The 3rd Annual Evaluation Conference of the Leading Program, University of Hyogo for the school year of 2015
    • Place of Presentation
      先端科学技術センター(兵庫県赤穂郡)
    • Year and Date
      2016-03-14
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Novel algorithm designed for identification of widely-diverse sequence motifs recognized by topoisomerase IIB2016

    • Author(s)
      Asuka Sugimoto, Jiyoung Kang, Yuhya Takahashi, Kakeru Sakabe, Mary Miuyaji, , Kimiko M. Tsutsui, Ken Tsutsui, Masaru Tateno
    • Organizer
      The 3rd Annual Evaluation Conference of the Leading Program, University of Hyogo for the school year of 2015
    • Place of Presentation
      先端科学技術センター(兵庫県赤穂郡)
    • Year and Date
      2016-03-14
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Development and application on informatical system for identification of functional structure in eukaryotic genomes2016

    • Author(s)
      Yuhya Takahashi, Jiyoung Kang, Masaru Tateno
    • Organizer
      The 3rd Annual Evaluation Conference of the Leading Program, University of Hyogo for the school year of 2015
    • Place of Presentation
      先端科学技術センター(兵庫県赤穂郡)
    • Year and Date
      2016-03-14
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Novel algorithm for efficiently-extended sampling in multivariate analysis of biochemical and bioinformatical experimental data2016

    • Author(s)
      Jiyoung Kang, Masaru Tateno
    • Organizer
      The 3rd Annual Evaluation Conference of the Leading Program, University of Hyogo for the school year of 2015
    • Place of Presentation
      先端科学技術センター(兵庫県赤穂郡)
    • Year and Date
      2016-03-14
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Theoretical investigation of biological mechanisms based on quantum mechanical and information mathematical sciences (oral)2015

    • Author(s)
      Masaru Tateno
    • Organizer
      3rd International Picobiology Institute Symposium
    • Place of Presentation
      先端科学技術センター(兵庫県赤穂郡)
    • Year and Date
      2015-12-08
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Novel algorithm for protein-protein docking based on identification of interfacial hydrogen bond network2015

    • Author(s)
      Jiyoung Kang, Masaru Tateno
    • Organizer
      3rd International Picobiology Institute Symposium
    • Place of Presentation
      先端科学技術センター(兵庫県赤穂郡)
    • Year and Date
      2015-12-08
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Structural modeling of supercoiled DNA recognition peptide complexed wth crossover DNA2015

    • Author(s)
      Kakeru Sakabe, Jiyoung Kang, Kazuhiko Yamasaki, Masaru Tateno
    • Organizer
      3rd International Picobiology Institute Symposium
    • Place of Presentation
      先端科学技術センター(兵庫県赤穂郡)
    • Year and Date
      2015-12-08
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Identification of topoisomerase IIB recognition motifs using novel scheme designed for that of widely-diverse sequences2015

    • Author(s)
      Asuka Sugimoto, Jiyoung Kang, Yuhya Takahashi, Kakeru Sakabe, Mary Miuyaji, , Kimiko M. Tsutsui, Ken Tsutsui, Masaru Tateno
    • Organizer
      3rd International Picobiology Institute Symposium
    • Place of Presentation
      先端科学技術センター(兵庫県赤穂郡)
    • Year and Date
      2015-12-08
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Novel algorithm for identification of gene clusters in eukaryotic genome DNA2015

    • Author(s)
      Yuhya Takahashi, Jiyoung Kang, Masaru Tateno
    • Organizer
      3rd International Picobiology Institute Symposium
    • Place of Presentation
      先端科学技術センター(兵庫県赤穂郡)
    • Year and Date
      2015-12-08
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Theoretical analysis of proton transfer mechanisms of photosystem II employing hybrid quantum molecular dynamics simulation2015

    • Author(s)
      Atsushi Nakamura, Jiyoung Kang, Yasufumi Umena, Keisuke Kawakami, Shen Jian-Ren, Nobuo Kamiyama, Masaru Tateno
    • Organizer
      3rd International Picobiology Institute Symposium
    • Place of Presentation
      先端科学技術センター(兵庫県赤穂郡)
    • Year and Date
      2015-12-08
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Theoretical identification of electronic structures responsible for proton-transfer-coupled-electron-transfer between proximal cluster and cluster and catalytic center in membrane bound hydrogenases2015

    • Author(s)
      Jaehyun Kim, Jiyoung Kang, Masaru Tateno
    • Organizer
      3rd International Picobiology Institute Symposium
    • Place of Presentation
      先端科学技術センター(兵庫県赤穂郡)
    • Year and Date
      2015-12-08
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Computational study of dynamical mechanism of substrate dislocation in binuclear center of cytochrome c oxidase2015

    • Author(s)
      Ryuichiro Terada, Jiyoung Kang, Masaru Tateno
    • Organizer
      3rd International Picobiology Institute Symposium
    • Place of Presentation
      先端科学技術センター(兵庫県赤穂郡)
    • Year and Date
      2015-12-08
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Novel theoretical scheme for analysis of functional mechanism of biological systems based on identification of information flow modulated by Maxwell's deamon2015

    • Author(s)
      Takuya Sumi, Jiyoung Kang, Masaru Tateno
    • Organizer
      3rd International Picobiology Institute Symposium
    • Place of Presentation
      先端科学技術センター(兵庫県赤穂郡)
    • Year and Date
      2015-12-08
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Effects of hydroxide ligand in proximal cluster of membrane bound hydrogenases (MBH) (oral)2015

    • Author(s)
      Jaehyun Kim, Jiyoung Kang, Masaru Tateno
    • Organizer
      第38回日本分子生物学会年会 第88回日本生化学大会 2015
    • Place of Presentation
      神戸ポートアイランド(兵庫県神戸市)
    • Year and Date
      2015-12-01
    • Related Report
      2015 Annual Research Report
  • [Presentation] Effects of hydroxide ligand in proximal cluster of membrane bound hydrogenases (MBH) (poster)2015

    • Author(s)
      Jaehyun Kim, Jiyoung Kang, Masaru Tateno
    • Organizer
      第38回日本分子生物学会年会 第88回日本生化学大会 2015
    • Place of Presentation
      神戸ポートアイランド(兵庫県神戸市)
    • Year and Date
      2015-12-01
    • Related Report
      2015 Annual Research Report
  • [Presentation] Hybrid quantum molecular dynamics study of mechanisms of ligand recognition by bovine cytochrome c oxidase2015

    • Author(s)
      Jiyoung Kang, Toru Matsuoka, Masaru Tateno
    • Organizer
      第38回日本分子生物学会年会 第88回日本生化学大会 2015
    • Place of Presentation
      神戸ポートアイランド(兵庫県神戸市)
    • Year and Date
      2015-12-01
    • Related Report
      2015 Annual Research Report
  • [Presentation] Proton transfer mechanisms in photosystem II : hybrid ab initio quantum mechanics study2015

    • Author(s)
      Atushi Nakamura, Jiyoung Kang, Yasufumi Umena, Keisuke Kawakami, Jian-Ren, Nobuo Kamiyama, Masaru Tateno
    • Organizer
      第38回日本分子生物学会年会 第88回日本生化学大会 2015
    • Place of Presentation
      神戸ポートアイランド(兵庫県神戸市)
    • Year and Date
      2015-12-01
    • Related Report
      2015 Annual Research Report
  • [Presentation] Novel algorithm for identification of gene clusters in whole genome DNA sequences2015

    • Author(s)
      Yuhya Takahashi, Jiyoung Kang, Masaru Tateno
    • Organizer
      第38回日本分子生物学会年会 第88回日本生化学大会 2015
    • Place of Presentation
      神戸ポートアイランド(兵庫県神戸市)
    • Year and Date
      2015-12-01
    • Related Report
      2015 Annual Research Report
  • [Presentation] Novel algorithm for protein-protein docking based on identification of interfacial hydrogen bond network2015

    • Author(s)
      Masaru Tateno, Takuya Takeda, Jiyoung Kang
    • Organizer
      第38回日本分子生物学会年会 第88回日本生化学大会 2015
    • Place of Presentation
      神戸ポートアイランド(兵庫県神戸市)
    • Year and Date
      2015-12-01
    • Related Report
      2015 Annual Research Report
  • [Presentation] Structural modeling of negatively-supercoiled DNA recognition peptide complexed with crossover DNA2015

    • Author(s)
      Kakeru Sakabe, Jiyoung Kang, Kazuhiko Yamasaki, Kuniaki Sano, Kimiko M. Tsutsui, Ken Tsutsui, Masaru Tateno
    • Organizer
      第38回日本分子生物学会年会 第88回日本生化学大会 2015
    • Place of Presentation
      神戸ポートアイランド(兵庫県神戸市)
    • Year and Date
      2015-12-01
    • Related Report
      2015 Annual Research Report
  • [Presentation] Novel strategy for genome-wide identification of widely-diverse transcriptional regulation motifs (oral)2015

    • Author(s)
      Asuka Sugimoto, Jiyoung Kang, Yuhya Takahashi, Mary Miuyaji, Ryohei Furuta, Kuniaki Sano, Kimiko M. Tsutsui, Ken Tsutsui, Masaru Tateno
    • Organizer
      生命医薬情報学連合大会2015年大会
    • Place of Presentation
      京都大学宇治キャンパスおうばくプラザ(京都府宇治市)
    • Year and Date
      2015-10-29
    • Related Report
      2015 Annual Research Report
  • [Presentation] Novel algorithm for identification of gene clusters in whole genome DNA sequences (oral)2015

    • Author(s)
      Yuhya Takahashi, Jiyoung Kang, Masaru Tateno
    • Organizer
      生命医薬情報学連合大会2015年大会
    • Place of Presentation
      京都大学宇治キャンパスおうばくプラザ(京都府宇治市)
    • Year and Date
      2015-10-29
    • Related Report
      2015 Annual Research Report
  • [Presentation] Development of structural analysis system of protein-protein complexes based on identification of hydrogen bond network s2015

    • Author(s)
      Jiyoung Kang, Takuya Takeda, Masaru Tateno
    • Organizer
      生命医薬情報学連合大会2015年大会
    • Place of Presentation
      京都大学宇治キャンパスおうばくプラザ(京都府宇治市)
    • Year and Date
      2015-10-29
    • Related Report
      2015 Annual Research Report
  • [Presentation] Novel algorithm for identification of gene clusters in whole genome DNA sequences (poster)2015

    • Author(s)
      Yuhya Takahashi, Jiyoung Kang, Masaru Tateno
    • Organizer
      生命医薬情報学連合大会2015年大会
    • Place of Presentation
      京都大学宇治キャンパスおうばくプラザ(京都府宇治市)
    • Year and Date
      2015-10-29
    • Related Report
      2015 Annual Research Report
  • [Presentation] Novel strategy for genome-wide identification of widely-diverse transcriptional regulation motifs (poster)2015

    • Author(s)
      Asuka Sugimoto, Jiyoung Kang, Yuhya Takahashi, Mary Miuyaji, Ryohei Furuta, Kuniaki Sano, Kimiko M. Tsutsui, Ken Tsutsui, Masaru Tateno
    • Organizer
      生命医薬情報学連合大会2015年大会
    • Place of Presentation
      京都大学宇治キャンパスおうばくプラザ(京都府宇治市)
    • Year and Date
      2015-10-29
    • Related Report
      2015 Annual Research Report
  • [Presentation] Electronic structures responsible for proton transfer coupled electron transfer between proximal cluster and catalytic center in membrane bound hydrogenases (MBH) (oral)2015

    • Author(s)
      Jaehyun Kim, Jiyoung Kang, Masaru Tateno
    • Organizer
      Science and Business 2nd Joint Symposium
    • Place of Presentation
      先端科学技術センター(兵庫県赤穂郡)
    • Year and Date
      2015-10-22
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Improvements and applications of hybrid ab initio quantum mechanics/molecular mechanics molecular dynamics simulation of biological macromolecular systems (oral)2015

    • Author(s)
      Kakeru Sakabe, Jiyoung Kang, Masaru Tateno
    • Organizer
      Science and Business 2nd Joint Symposium
    • Place of Presentation
      先端科学技術センター(兵庫県赤穂郡)
    • Year and Date
      2015-10-22
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Electronic structures responsible for proton transfer coupled electron transfer between proximal cluster and catalytic center in membrane bound hydrogenases (MBH) (poster)2015

    • Author(s)
      Jaehyun Kim, Jiyoung Kang, Masaru Tateno
    • Organizer
      Science and Business 2nd Joint Symposium
    • Place of Presentation
      先端科学技術センター(兵庫県赤穂郡)
    • Year and Date
      2015-10-22
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Improvements and applications of hybrid ab initio quantum mechanics/molecular mechanics molecular dynamics simulation of biological macromolecular systems (poster)2015

    • Author(s)
      Kakeru Sakabe, Jiyoung Kang, Masaru Tateno
    • Organizer
      Science and Business 2nd Joint Symposium
    • Place of Presentation
      先端科学技術センター(兵庫県赤穂郡)
    • Year and Date
      2015-10-22
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Development of structural analysis system of protein-protein complexes based on identification of hydrogen bond network (oral)2015

    • Author(s)
      Masaru Tateno, Takuya Takeda, Jiyoung Kang
    • Organizer
      第53回生物物理学会年会 2015
    • Place of Presentation
      金沢大学角間キャンパス(石川県金沢市)
    • Year and Date
      2015-09-13
    • Related Report
      2015 Annual Research Report
  • [Presentation] Mechanisms of selection of channel for substrate transport in GatCAB (oral)2015

    • Author(s)
      Jiyoung Kang, Masaru Tateno
    • Organizer
      第53回生物物理学会年会 2015
    • Place of Presentation
      金沢大学角間キャンパス(石川県金沢市)
    • Year and Date
      2015-09-13
    • Related Report
      2015 Annual Research Report
  • [Presentation] Novel algorithm for identification of gene clusters in whole genome DNA sequences by combining rigorous and heuristic schemes (oral)2015

    • Author(s)
      Yuhya Takahashi, Jiyoung Kang, Masaru Tateno
    • Organizer
      第53回生物物理学会年会 2015
    • Place of Presentation
      金沢大学角間キャンパス(石川県金沢市)
    • Year and Date
      2015-09-13
    • Related Report
      2015 Annual Research Report
  • [Presentation] Structural modeling of negatively supercoiled DNA recognition peptide with crossover DNA (oral)2015

    • Author(s)
      Kakeru Sakabe, Jiyoung Kang, Masaru Tateno
    • Organizer
      第53回生物物理学会年会 2015
    • Place of Presentation
      金沢大学角間キャンパス(石川県金沢市)
    • Year and Date
      2015-09-13
    • Related Report
      2015 Annual Research Report
  • [Presentation] Proton transfer mechanisms of photosystem II : Hybrid ab initio quantum mechanics study2015

    • Author(s)
      Atsushi Nakamura, Jiyoung Kang, Yasufumi Umena, Keisuke Kawakami, Jian-Ren, Nobuo Kamiyama, Masaru Tateno
    • Organizer
      第53回生物物理学会年会 2015
    • Place of Presentation
      金沢大学角間キャンパス(石川県金沢市)
    • Year and Date
      2015-09-13
    • Related Report
      2015 Annual Research Report
  • [Presentation] Determination of configurations of ligands bound to CuB site of bovine cytochrome c oxidases by using spatial mapping technique of energy2015

    • Author(s)
      Kang, J., Matsuoka, T., and Tateno, M.
    • Organizer
      The annual evaluation conference of the leading program
    • Place of Presentation
      Center of Advanced Sciences and Technologies (CAST) (兵庫)
    • Year and Date
      2015-03-16 – 2015-03-17
    • Related Report
      2014 Annual Research Report
  • [Presentation] Propagation pathways of structural changes for T/R transition: Modulation mechanism of O2 affinity of human adult haemoglobin2015

    • Author(s)
      Tateno, M., Itagaki, T., and Kang, J.
    • Organizer
      The annual evaluation conference of the leading program
    • Place of Presentation
      Center of Advanced Sciences and Technologies (CAST) (兵庫)
    • Year and Date
      2015-03-16 – 2015-03-17
    • Related Report
      2014 Annual Research Report
  • [Presentation] Development and application of structural analysis system of protein- protein complexes based on identifications of hydrogen bond network2015

    • Author(s)
      Takeda, T., Kang, J., and Tateno, M.
    • Organizer
      The annual evaluation conference of the leading program
    • Place of Presentation
      Center of Advanced Sciences and Technologies (CAST) (兵庫)
    • Year and Date
      2015-03-16 – 2015-03-17
    • Related Report
      2014 Annual Research Report
  • [Presentation] Structural modeling of negatively supercoiled DNA recognition peptide complexed with crossover double stranded DNA molecules2015

    • Author(s)
      Sato, C., Kang, J., and Tateno, M.
    • Organizer
      The annual evaluation conference of the leading program
    • Place of Presentation
      Center of Advanced Sciences and Technologies (CAST) (兵庫)
    • Year and Date
      2015-03-16 – 2015-03-17
    • Related Report
      2014 Annual Research Report
  • [Presentation] Identification of DNA binding motifs of topoisomerase IIb in rat whole genome DNA sequence : Mechanism of DNA recognition2015

    • Author(s)
      Sugimoto, A., Kang, J., and Tateno, M.
    • Organizer
      The annual evaluation conference of the leading program
    • Place of Presentation
      Center of Advanced Sciences and Technologies (CAST) (兵庫)
    • Year and Date
      2015-03-16 – 2015-03-17
    • Related Report
      2014 Annual Research Report
  • [Presentation] Novel algorithm for identification of gene clusters in whole genome DNA sequences by combining rigorous and heuristic schemes2015

    • Author(s)
      Takahashi, Y., Kang, J., and Tateno, M.
    • Organizer
      The annual evaluation conference of the leading program
    • Place of Presentation
      Center of Advanced Sciences and Technologies (CAST) (兵庫)
    • Year and Date
      2015-03-16 – 2015-03-17
    • Related Report
      2014 Annual Research Report
  • [Presentation] Theoretical analysis of proton transfer mechanisms of photosystem II employing hybrid quantum molecular dynamics simulation2015

    • Author(s)
      Nakamura, A., Kang, J., and Tateno, M.
    • Organizer
      The annual evaluation conference of the leading program
    • Place of Presentation
      Center of Advanced Sciences and Technologies (CAST) (兵庫)
    • Year and Date
      2015-03-16 – 2015-03-17
    • Related Report
      2014 Annual Research Report
  • [Presentation] Comparison of electronic structures of the proximal cluster in membrane bound hydrogenases (MBH) in the presence and absence of a hydroxide ligand2015

    • Author(s)
      Kim, J., Kang, J., and Tateno, M.
    • Organizer
      The annual evaluation conference of the leading program
    • Place of Presentation
      Center of Advanced Sciences and Technologies (CAST) (兵庫)
    • Year and Date
      2015-03-16 – 2015-03-17
    • Related Report
      2014 Annual Research Report
  • [Presentation] Dual catalytic pathways identified in complex of oncogenic product Ras and Ras-GAP2015

    • Author(s)
      Sakabe, K., Kang, J., and Tateno, M.
    • Organizer
      The annual evaluation conference of the leading program
    • Place of Presentation
      Center of Advanced Sciences and Technologies (CAST) (兵庫)
    • Year and Date
      2015-03-16 – 2015-03-17
    • Related Report
      2014 Annual Research Report
  • [Presentation] トポイソメラーゼIIβの酵素活性と核内動態はC末端ドメインへのRNAの結合によって制御されている2014

    • Author(s)
      小野田彰久、細谷 修、佐野訓明、宮地まり、筒井 研、筒井公子
    • Organizer
      第32回染色体ワークショップ・第13回細胞核ダイナミクス研究会
    • Place of Presentation
      安芸グランドホテル(広島県)
    • Year and Date
      2014-12-15 – 2014-12-17
    • Related Report
      2014 Annual Research Report
  • [Presentation] A novel domain of topoisomerase IIb regulates nuclear dynamics and catalytic activity of the enzyme by binding to RNA2014

    • Author(s)
      Tsutsui, K.M., Hosoya, O., Onoda, A., Sano, K., Kimura, H., Miyaji, M., and Tsutsui, K.
    • Organizer
      第37回日本分子生物学会年会
    • Place of Presentation
      パシフィコ横浜(横浜)
    • Year and Date
      2014-11-25 – 2014-11-27
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] DNAトポイソメラーゼIIβによる核内構造変化と遺伝子発現調節2014

    • Author(s)
      古田良平、宮地まり、細谷 修、佐野訓明、筒井公子、筒井 研
    • Organizer
      第37回日本分子生物学会年会
    • Place of Presentation
      パシフィコ横浜(横浜)
    • Year and Date
      2014-11-25 – 2014-11-27
    • Related Report
      2014 Annual Research Report
  • [Presentation] RNA regulates nuclear dynamics and catalytic activity of topoisomerase IIbeta by binding to a novel domain of the enzyme2014

    • Author(s)
      Tsutsui, K.M., Hosoya, O., Onoda, A., Sano, K., Kawano, S., Miyaji, M., and Tsutsui, K.
    • Organizer
      Cell Symposia “Regulatory RNAs”
    • Place of Presentation
      Berkeley (US)
    • Year and Date
      2014-10-19 – 2014-10-21
    • Related Report
      2014 Annual Research Report
  • [Presentation] RNAによるDNAトポイソメラーゼIIαの酵素活性制御機構の解析2014

    • Author(s)
      加藤佑梨、岡朶夏海、藤本薫平、池田正五、筒井公子、筒井 研、河野真二
    • Organizer
      第87回日本生化学会大会
    • Place of Presentation
      京都国際会館(京都)
    • Year and Date
      2014-10-15 – 2014-10-18
    • Related Report
      2014 Annual Research Report
  • [Presentation] Theoretical analysis of functional mechanisms of hydrogenases using ab initio electronic calculation and molecular mechanics calculations2014

    • Author(s)
      Kim, J., Kang, J., and Tateno, M.
    • Organizer
      2nd International Picobiology Institute Symposium
    • Place of Presentation
      Center of Advanced Sciences and Technologies (CAST) (兵庫)
    • Year and Date
      2014-10-09 – 2014-10-10
    • Related Report
      2014 Annual Research Report
  • [Presentation] Modulation of atomic electron densities of cytosine base through proton dislocation for catalytic enhancement by M. HhaI DNA methyltransferase2014

    • Author(s)
      Kang, J., and Tateno, M.
    • Organizer
      2nd International Picobiology Institute Symposium
    • Place of Presentation
      Center of Advanced Sciences and Technologies (CAST) (兵庫)
    • Year and Date
      2014-10-09 – 2014-10-10
    • Related Report
      2014 Annual Research Report
  • [Presentation] Theoretical and computational investigations of functional mechanisms of biological macromolecules2014

    • Author(s)
      Masaru Tateno
    • Organizer
      International Picobiology Institute Symposium
    • Place of Presentation
      理化学研究所・放射光科学総合研究センター (兵庫県佐用郡佐用町)
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] 生命の計算科学: そのターゲットは?2014

    • Author(s)
      Masaru Tateno
    • Organizer
      第2回放射光と計算科学の研究会
    • Place of Presentation
      姫路じばさんびる (兵庫県姫路市南駅前町)
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] Development and application of novel algorithm for protein-protein docking simulation based on intermolecular hydrogen-bond networks2014

    • Author(s)
      Takuya Takeda, Jiyoung Kang, Masaru Tateno
    • Organizer
      International Picobiology Institute Symposium
    • Place of Presentation
      理化学研究所・放射光科学総合研究センター (兵庫県佐用郡佐用町)
    • Related Report
      2013 Annual Research Report
  • [Presentation] Novel computational scheme for structural determination of multiple conformational segments of biological macromolecules employing crystallographic electron density data in low resolution regions2014

    • Author(s)
      Kiyohito Kihira, Jiyoung Kang, Hiroshi Nishigami, Masaru Tateno, Tomitake Tsukihara
    • Organizer
      International Picobiology Institute Symposium
    • Place of Presentation
      理化学研究所・放射光科学総合研究センター (兵庫県佐用郡佐用町)
    • Related Report
      2013 Annual Research Report
  • [Presentation] Is allosteric mechanism really required for cooperative O2 affinity of human adult haemoglobin ?2014

    • Author(s)
      Tetsuhiko Itagaki, Jiyoung Kang, Masaru Tateno
    • Organizer
      International Picobiology Institute Symposium
    • Place of Presentation
      理化学研究所・放射光科学総合研究センター (兵庫県佐用郡佐用町)
    • Related Report
      2013 Annual Research Report
  • [Presentation] Development and application of ab initio identification system of transcription factor binding motif in genome-wide data2014

    • Author(s)
      Yuya Takahashi, Jiyoung Kang, Kim Kyoung-tark, Masaru Tateno
    • Organizer
      International Picobiology Institute Symposium
    • Place of Presentation
      理化学研究所・放射光科学総合研究センター (兵庫県佐用郡佐用町)
    • Related Report
      2013 Annual Research Report
  • [Presentation] Functional mechanism of bovine cytochrome c oxidase (I) -- Double-stratified architecture of CuA site for electron transfer2014

    • Author(s)
      Jiyoung Kang, Masaru Tateno
    • Organizer
      International Picobiology Institute Symposium
    • Place of Presentation
      理化学研究所・放射光科学総合研究センター (兵庫県佐用郡佐用町)
    • Related Report
      2013 Annual Research Report
  • [Presentation] Functional mechanism of bovine cytochrome c oxidase (II) -- Dynamical mechanism of ligand recognition2014

    • Author(s)
      Toru Matsuoka, Jiyoung Kang, Masaru Tateno
    • Organizer
      International Picobiology Institute Symposium
    • Place of Presentation
      理化学研究所・放射光科学総合研究センター (兵庫県佐用郡佐用町)
    • Related Report
      2013 Annual Research Report
  • [Presentation] Cation-π vs. Water-π : Theoretical evaluation of structural stability of the active center of T1 lipase and identification of a novel protein structural element2014

    • Author(s)
      Atsushi Nakamura, Jiyoung Kang, Masaru Tateno
    • Organizer
      International Picobiology Institute Symposium
    • Place of Presentation
      理化学研究所・放射光科学総合研究センター (兵庫県佐用郡佐用町)
    • Related Report
      2013 Annual Research Report
  • [Presentation] Dynamical mechanism of catalysis by complex of oncogenic product Ras and Ras-GAP2014

    • Author(s)
      Masaru Tateno, Tetsuhiko Itagaki, Jiyoung Kang
    • Organizer
      International Picobiology Institute Symposium
    • Place of Presentation
      理化学研究所・放射光科学総合研究センター (兵庫県佐用郡佐用町)
    • Related Report
      2013 Annual Research Report
  • [Presentation] Catalytic mechanism of complex of valyl-tRNA synthetase and mis-aminoacylated tRNA2014

    • Author(s)
      Kakeru Sakabe, Jiyoung Kang, Masaru Tateno
    • Organizer
      International Picobiology Institute Symposium
    • Place of Presentation
      理化学研究所・放射光科学総合研究センター (兵庫県佐用郡佐用町)
    • Related Report
      2013 Annual Research Report
  • [Presentation] Hybrid Catalysis of Protein and RNA Enzyme2013

    • Author(s)
      Masaru Tateno
    • Organizer
      Annual Global Congress of Catalysis
    • Place of Presentation
      Dalian (中国)
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] Theoretical Investigation of Catalytic Mechanisms of Biological Macromolecules: Toward Development of a Novel scheme for Molecular Design2013

    • Author(s)
      Masaru Tateno
    • Organizer
      Annual International Conference of Medichem
    • Place of Presentation
      Haikou (中国)
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] 量子と情報による生命の理解2013

    • Author(s)
      Masaru Tateno
    • Organizer
      第25回 異分野交流研究会
    • Place of Presentation
      アーバンエース三宮ビル (兵庫県神戸市中央区)
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] Multiple molecular dynamics simulations of human adult haemoglobin: Novel intra-molecular signal propagation pathways for nonlinear response in ligand-binding,2013

    • Author(s)
      Tetsuhiko Itagaki, Jiyoung Kang, Masaru Tateno
    • Organizer
      International Conference on Molecular Simulation 2013
    • Place of Presentation
      神戸国際会議場 (兵庫県神戸市中央区)
    • Related Report
      2013 Annual Research Report
  • [Presentation] Hybrid quantum mechanics (QM) / molecular mechanics (MM) molecular dynamics (MD) simulation of catalytic mechanism by complex of Ras and Ras-GAP: Full description of catalytic mechanisms2013

    • Author(s)
      Masaru Tateno, Tetsuhiko Itagaki, Jiyoung Kang
    • Organizer
      International Conference on Molecular Simulation 2013
    • Place of Presentation
      神戸国際会議場 (兵庫県神戸市中央区)
    • Related Report
      2013 Annual Research Report
  • [Presentation] Hybrid QM/MM simulation of bovine cytochrome c oxidase (II): Dynamical mechanisms of ligand recognition2013

    • Author(s)
      Toru Matsuoka, Jiyoung Kang, Masaru Tateno
    • Organizer
      International Conference on Molecular Simulation 2013
    • Place of Presentation
      神戸国際会議場 (兵庫県神戸市中央区)
    • Related Report
      2013 Annual Research Report
  • [Presentation] Cation-π vs. Water-π : Theoretical analysis of structural stability of the active center of T1 lipase employing a novel accurate and efficient description of effective potential2013

    • Author(s)
      Atsushi Nakamura, Jiyoung Kang, Masaru Tateno
    • Organizer
      International Conference on Molecular Simulation 2013
    • Place of Presentation
      神戸国際会議場 (兵庫県神戸市中央区)
    • Related Report
      2013 Annual Research Report
  • [Presentation] Hybrid QM/MM simulation of bovine cytochrome c oxidase (I) : Double-stratified architecture for electron transfer2013

    • Author(s)
      Jiyoung Kang, Masaru Tateno
    • Organizer
      International Conference on Molecular Simulation 2013
    • Place of Presentation
      神戸国際会議場 (兵庫県神戸市中央区)
    • Related Report
      2013 Annual Research Report
  • [Presentation] Catalytic mechanisms by Ras:hybrid quantum mechanics/molecular mechanics molecular dynamics simulations of the complex with the GAP2013

    • Author(s)
      Takuya Takeda, Tetsuhiko Itagaki, Jiyoung Kang, Masaru Tateno
    • 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 (鳥取市尚徳町)
    • Related Report
      2013 Annual Research Report
  • [Presentation] Theoretical analysis of fully-hydrated structures of human adult hemoglobin employing multiple molecular dynamics simulations2013

    • Author(s)
      Tetsuhiko Itagaki, Jiyoung Kang, Masaru Tateno
    • 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 (鳥取市尚徳町)
    • Related Report
      2013 Annual Research Report
  • [Presentation] Theoretical analysis of binding modes of CO ligand bound to the CuB site of bovine cytochrome c oxidase by using ab initio calculations2013

    • Author(s)
      Toru Matsuoka, Jiyoung Kang, Masaru Tateno
    • 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 (鳥取市尚徳町)
    • Related Report
      2013 Annual Research Report
  • [Presentation] Theoretical study of functional role of axial methionine ligand of CuA site in cytochrome c oxidases2013

    • Author(s)
      Jiyoung Kang, Masaru Tateno
    • 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 (鳥取市尚徳町)
    • Related Report
      2013 Annual Research Report
  • [Presentation] Unidirectional mechanistic valve for substrate transport in GatCAB revealed by multiple molecular dynamics simulations2013

    • Author(s)
      Masaru Tateno, Jiyoung Kang,
    • 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 (鳥取市尚徳町)
    • Related Report
      2013 Annual Research Report
  • [Presentation] Novel computational system for protein-protein docking simulation based on informatical extensive search of intermolecular hydrogen bond networks2013

    • Author(s)
      Takuya Takeda, Jiyoung Kang, Kazushi Kitta, Masaru Tateno
    • Organizer
      第86回日本生化学会年会
    • Place of Presentation
      パシィフィコ横浜 (横浜市西区)
    • Related Report
      2013 Annual Research Report
  • [Presentation] Modulation mechanism of oxygen affinity of human adult hemoglobin through novel pathways for structural propagation in T/R transition revealed by multiple molecular dynamics simulations2013

    • Author(s)
      Tetsuhiko Itagaki, Jiyoung Kang, Masaru Tateno
    • Organizer
      第86回日本生化学会年会
    • Place of Presentation
      パシィフィコ横浜 (横浜市西区)
    • Related Report
      2013 Annual Research Report
  • [Presentation] Dynamical enzymatic mechanisms of GTP hydrolysis by complex of oncogenic product Ras and Ras-GAP: hybrid quantum mechanics / molecular mechanics molecular dynamics simulations2013

    • Author(s)
      Masaru Tateno, Jiyoung Kang, Kyoung-Tark Kim
    • Organizer
      第86回日本生化学会年会
    • Place of Presentation
      パシィフィコ横浜 (横浜市西区)
    • Related Report
      2013 Annual Research Report
  • [Presentation] Dynamical mechanisms of ligand recognition of bovine cytochrome c oxidase: theoretical analysis using hybrid quantum mechanics / molecular mechanics (QM/MM) molecular dynamics (MD) simulation2013

    • Author(s)
      Toru Matsuoka, Jiyoung Kang, Masaru Tateno
    • Organizer
      第86回日本生化学会年会
    • Place of Presentation
      パシィフィコ横浜 (横浜市西区)
    • Related Report
      2013 Annual Research Report
  • [Presentation] MODIC2: ab initio identification system of transcription factor binding motifs in genome-wide data2013

    • Author(s)
      Yuya Takahashi, Jiyoung Kang, Kyoung-tark Kim, Masaru Tateno
    • Organizer
      第86回日本生化学大会
    • Place of Presentation
      パシィフィコ横浜 (横浜市西区)
    • Related Report
      2013 Annual Research Report
  • [Presentation] A novel algorithm for structural determination of multiple conformational segments in biological macromolecules employing electron density data involved in small scattering-angle regions2013

    • Author(s)
      Kiyohito Kihira, Jiyoung Kang, Hiroshi Nishigami, Masaru Tateno, Tomitake Tsukihara
    • Organizer
      第86回日本生化学会大会
    • Place of Presentation
      パシィフィコ横浜 (横浜市西区)
    • Related Report
      2013 Annual Research Report
  • [Presentation] SBP75の選択的DNA高次構造認識2013

    • Author(s)
      佐野訓明、山崎和彦、筒井公子、筒井 研
    • Organizer
      第86回 日本生化学会大会
    • Place of Presentation
      パシィフィコ横浜 (横浜市西区)
    • Related Report
      2013 Annual Research Report
  • [Presentation] DNA トポイソメラーゼIIβのC末端領域による酵素反応制御機構の解析2013

    • Author(s)
      河野真二、加藤佑梨、小野田彰久、木山和子、池田正五、筒井公子、筒井 研
    • Organizer
      第86回 日本生化学会大会
    • Place of Presentation
      パシィフィコ横浜 (横浜市西区)
    • Related Report
      2013 Annual Research Report
  • [Presentation] Biochemical and structural basis of epigenetic regulation: dynamical catalytic mechanism of HhaI DNA methyltransferase revealed by quantum mechanics/molecular mechanics molecular dynamics simulations2013

    • Author(s)
      Jiyoung Kang and Masaru Tateno
    • Organizer
      第86回日本生化学会大会
    • Place of Presentation
      パシィフィコ横浜 (横浜市西区)
    • Related Report
      2013 Annual Research Report
  • [Presentation] Novel computational system for protein-protein docking simulation using the intermolecular hydrogen-bond networks2013

    • Author(s)
      Takuya Takeda, Jiyoung Kang, Kazushi Kitta, Masaru Tateno
    • Organizer
      日本バイオインフォマティクス学会2013年年会&第2回生命医薬情報学連大会
    • Place of Presentation
      タワーホール船堀 (東京都江戸川区)
    • Related Report
      2013 Annual Research Report
  • [Presentation] Development and evaluation of a novel ab initio identification system of transcription factor binding motifs in genome DNA sequences2013

    • Author(s)
      Masaru Tateno, Ryu Nakaki and Jiyoung Kang
    • Organizer
      日本バイオインフォマティクス学会2013年年会&第2回生命医薬情報学連合大会
    • Place of Presentation
      タワーホール船堀 (東京都江戸川区)
    • Related Report
      2013 Annual Research Report
  • [Presentation] Novel structural determination algorithm of multiple conformational segments of biological macromolecules employing crystallographic electron density data in low-angle/low-resolution regions2013

    • Author(s)
      Jiyoung Kang, Kiyohito Kihira, Hiroshi Nishigami, Masaru Tateno and Tomitake Tsukihara
    • Organizer
      日本バイオインフォマティクス学会2013年年会&第2回生命医薬情報学連合大会
    • Place of Presentation
      タワーホール船堀 (東京都江戸川区)
    • Related Report
      2013 Annual Research Report
  • [Presentation] Novel algorithm for protein-protein docking simulation on the basis of intermolecular hydrogen-bond networks2013

    • Author(s)
      Takuya Takeda, Jiyoung Kang, Kazushi Kitta, Masaru Tateno
    • Organizer
      第36回日本分子生物学会年会
    • Place of Presentation
      神戸国際会議場 (兵庫県神戸市中央区)
    • Related Report
      2013 Annual Research Report
  • [Presentation] Modulation mechanism of oxygen affinity of human adult hemoglobin: Novel structural propagation pathways in T/R transition identified by multiple molecular dynamics simulations2013

    • Author(s)
      Tetsuhiko Itagaki, Jiyoung Kang, Masaru Tateno
    • Organizer
      第36回日本分子生物学会年会
    • Place of Presentation
      神戸国際会議場 (兵庫県神戸市中央区)
    • Related Report
      2013 Annual Research Report
  • [Presentation] Full description of reaction mechanism of GTP hydrolysis by complex of Ras and Ras-GAP revealed by hybrid quantum mechanics / molecular mechanics molecular dynamics simulations2013

    • Author(s)
      Masaru Tateno, Tetsuhiko Itagaki, Jiyoung Kang
    • Organizer
      第36回日本分子生物学会年会
    • Place of Presentation
      神戸国際会議場 (兵庫県神戸市中央区)
    • Related Report
      2013 Annual Research Report
  • [Presentation] Hybrid quantum molecular dynamics study of structural changes of bovine cytochrome c oxidase induced by ligand-binding,2013

    • Author(s)
      Toru Matsuoka, Jiyoung Kang, Masaru Tateno
    • Organizer
      第36回日本分子生物学会年会
    • Place of Presentation
      神戸国際会議場 (兵庫県神戸市中央区)
    • Related Report
      2013 Annual Research Report
  • [Presentation] Novel structural determination scheme of multiple conformational segments of biological macromolecules employing crystallographic electron density data in low-angle/low-resolution regions2013

    • Author(s)
      Kiyohito Kihira, Jiyoung Kang, Hiroshi Nishigami, Masaru Tateno, Tomitake Tukihara
    • Organizer
      第36回日本分子生物学会年会
    • Place of Presentation
      神戸国際会議場 (兵庫県神戸市中央区)
    • Related Report
      2013 Annual Research Report
  • [Presentation] Dynamical analysis of catalytic reaction of complex of valyl-tRNA synthetase and its cognate tRNA using hybrid ab initio quantum mechanics molecular dynamics simulation2013

    • Author(s)
      Kakeru Sakabe, Jiyoung Kang, Masaru Tateno
    • Organizer
      第36回日本分子生物学会年会
    • Place of Presentation
      神戸国際会議場 (兵庫県神戸市中央区)
    • Related Report
      2013 Annual Research Report
  • [Presentation] Development and application of ab initio transcription factor binding motif finder from genome-wide data2013

    • Author(s)
      Yuya Takahashi, Jiyoung Kang, Kyoung-tark Kim, Masaru Tateno
    • Organizer
      第36回日本分子生物学会年会
    • Place of Presentation
      神戸国際会議場 (兵庫県神戸市中央区)
    • Related Report
      2013 Annual Research Report
  • [Presentation] Theoretical study of catalytic mechanism of M. HhaI DNA methyltransferase using hybrid quantum mechanics molecular dynamics simulations2013

    • Author(s)
      Jiyoung Kang, Masaru Tateno
    • Organizer
      第36回日本分子生物学会年会
    • Place of Presentation
      神戸国際会議場 (兵庫県神戸市中央区)
    • Related Report
      2013 Annual Research Report
  • [Presentation] DNAトポイソメラーゼIIβによる遺伝子制御と核構造2013

    • Author(s)
      古田良平、宮地まり、佐野訓明、細谷 修、筒井公子、筒井 研
    • Organizer
      第36回 日本分子生物学会
    • Place of Presentation
      神戸国際会議場 (兵庫県神戸市中央区)
    • Related Report
      2013 Annual Research Report
  • [Remarks] MODIC2 : ab initio Motif Finder(ウェブ解析サービスの提供)

    • URL

      http://164.125.114.200/~jykang/modic.html

    • Related Report
      2016 Annual Research Report
  • [Remarks] MODIC2: 転写制御配列・自動同定解析システム(自動解析ウェブ・サービスシステムの開発)

    • URL

      http://lat.pusan.ac.kr/~jykang/modic.html

    • Related Report
      2013 Annual Research Report

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Published: 2013-05-21   Modified: 2019-07-29  

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