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Elucidation of information-processing mechanisms during transcription cycle using computational and information sciences

Planned Research

Project AreaIntegral understanding of the mechanism of transcription cycle through quantitative, high-resolution approaches
Project/Area Number 24118008
Research Category

Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)

Allocation TypeSingle-year Grants
Review Section Biological Sciences
Research InstitutionOsaka University

Principal Investigator

NAKAMURA Haruki  大阪大学, たんぱく質研究所, 教授 (80134485)

Co-Investigator(Kenkyū-buntansha) 藤井 聡  九州工業大学, 大学院情報工学研究院, 助教 (40452825)
皿井 明倫  九州工業大学, その他の研究科, 教授 (20221286)
Co-Investigator(Renkei-kenkyūsha) KAMIYA Narutoshi  兵庫県立大学, シミュレーション学研究科, 特任教授 (80420462)
KONO Hidetoshi  量子科学技術研究開発機構, 量子生命科学研究部, 生体分子シミュレーショングループリーダー (40291918)
KASAHARA Kota  立命館大学, 生命科学部, 助教 (90634965)
Research Collaborator IIDA Midori  
Project Period (FY) 2012-06-28 – 2017-03-31
Project Status Completed (Fiscal Year 2016)
Budget Amount *help
¥178,230,000 (Direct Cost: ¥137,100,000、Indirect Cost: ¥41,130,000)
Fiscal Year 2016: ¥34,060,000 (Direct Cost: ¥26,200,000、Indirect Cost: ¥7,860,000)
Fiscal Year 2015: ¥34,060,000 (Direct Cost: ¥26,200,000、Indirect Cost: ¥7,860,000)
Fiscal Year 2014: ¥34,190,000 (Direct Cost: ¥26,300,000、Indirect Cost: ¥7,890,000)
Fiscal Year 2013: ¥33,930,000 (Direct Cost: ¥26,100,000、Indirect Cost: ¥7,830,000)
Fiscal Year 2012: ¥41,990,000 (Direct Cost: ¥32,300,000、Indirect Cost: ¥9,690,000)
Keywords転写因子 / 遺伝子 / 分子動力学計算 / 生体生命情報学 / 生物物理 / 生体分子 / 蛋白質 / ポリメラーゼ / ヌクレオソーム
Outline of Final Research Achievements

In order to reveal the dynamic properties of the information transduction at the transcription cycle, new computational and informatics approaches have been developed. For the transcription factors in the enhanceosome and the relation to nucleosome, dynamic structural changes and the stabilities of the supramolecular complexes were analyzed so as to analyze the actual mechanisms in the transcription cycle. In addition, to extract biologically important and meaningful information and knowledges from the large scale data produced by the members of the research groups of the Transcription Cycle, mechanisms of transcription regulation were investigated based on the experimental data of Micro-array, RNA-seq, and ChIP-seq.

Report

(6 results)
  • 2016 Annual Research Report   Final Research Report ( PDF )
  • 2015 Annual Research Report
  • 2014 Annual Research Report
  • 2013 Annual Research Report
  • 2012 Annual Research Report
  • Research Products

    (156 results)

All 2017 2016 2015 2014 2013 2012 Other

All Journal Article (34 results) (of which Int'l Joint Research: 7 results,  Peer Reviewed: 34 results,  Open Access: 26 results,  Acknowledgement Compliant: 16 results) Presentation (112 results) (of which Int'l Joint Research: 12 results,  Invited: 24 results) Book (4 results) Remarks (6 results)

  • [Journal Article] Enhancement of canonical sampling by virtual-state transitions2017

    • Author(s)
      Junichi Higo, Kota Kasahara, Bhaskar Dasgupta, Haruki Nakamura
    • Journal Title

      J. Chem. Phys.

      Volume: 146 Issue: 4 Pages: 44104-44104

    • DOI

      10.1063/1.4974087

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Molecular mechanisms of cooperative binding of transcription factors Runx1-CBFβ-Ets1 on the TCRα gene enhancer2017

    • Author(s)
      Kasahara K, Shiina M, Fukuda I, Ogata K, Nakamura H
    • Journal Title

      PloS One

      Volume: 12 Issue: 2 Pages: e0172654-e0172654

    • DOI

      10.1371/journal.pone.0172654

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] mDCC_tools: Characterizing Multi-modal Atomic Motions in Molecular Dynamics Trajectories2016

    • Author(s)
      Kota Kasahara, Neetha Mohan, Ikuo Fukuda, Haruki Nakamura
    • Journal Title

      Bioinformatics

      Volume: 32 Issue: 16 Pages: 2531-2533

    • DOI

      10.1093/bioinformatics/btw129

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Elastic properties of dynein motor domain obtained from all-atom molecular dynamics simulations2016

    • Author(s)
      Narutoshi Kamiya, Tadaaki Mashimo, Yu Takano, Takahide Kon, Genji Kurisu, Haruki Nakamura
    • Journal Title

      Protein Engineering, Design and Selection

      Volume: 29 Issue: 8 Pages: 317-325

    • DOI

      10.1093/protein/gzw022

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Rapid and efficient analysis of gene function using CRISPR-Cas9 in Xenopus tropicalis founders2016

    • Author(s)
      Shigeta, Mitsuki; Sakane, Yuto; Iida, Midori; Suzuki, Miyuki; Kashiwagi, Keiko; Kashiwagi, Akihiko; Fujii, Satoshi; Yamamoto, Takashi; Suzuki, Ken-ichi
    • Journal Title

      Genes to Cells

      Volume: in press Issue: 7 Pages: 755-771

    • DOI

      10.1111/gtc.12379

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Revisiting Antibody Modeling Assessment for CDR-H3 loop2016

    • Author(s)
      Hiroshi Nishigami, Narutoshi Kamiya, Haruki Nakamura
    • Journal Title

      Protein Engineering, Design and Selection

      Volume: 29 Issue: 11 Pages: 477-484

    • DOI

      10.1093/protein/gzw028

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Identification of aryl hydrocarbon receptor signaling pathways altered in TCDD- treated red seabream embryos by transcriptome analysis2016

    • Author(s)
      Midori Iida, Satoshi Fujii, Masaya Uchida, , Hiroshi Nakamura, Yoshihiro Kagami, Tetsuro Agusa, Masashi Hirano, Su-Min Bak, Eun-Young Kim, Hisato Iwata
    • Journal Title

      Aquatic Toxicology

      Volume: 177 Pages: 156-170

    • DOI

      10.1016/j.aquatox.2016.05.014

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] myPresto/omegagene: a GPU-accelerated molecular dynamics simulator tailored for enhanced conformational sampling methods with a non-Ewald electrostatic scheme2016

    • Author(s)
      Kota Kasahara, Benson Ma, Kota Goto, Bhaskar Dasgupta, Junichi Higo, Ikuo Fukuda, Tadaaki Mashimo, Yutaka Akiyama, Haruki Nakamura
    • Journal Title

      Biophysics and Physicobiology

      Volume: 13 Issue: 0 Pages: 209-216

    • DOI

      10.2142/biophysico.13.0_209

    • NAID

      130007041560

    • ISSN
      2189-4779
    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] Variation of Free-Energy Landscape of the p53 C-terminal Domain Induced by Acetylation: Enhanced Conformational Sampling2016

    • Author(s)
      Shinji Iida, Tadaaki Mashimo, Takashi Kurosawa, Hironobu Hojo, Hiroya Muta, Yuji Goto, Yoshifumi Fukunishi, Haruki Nakamura, Junichi Higo
    • Journal Title

      J. Comput. Chem.

      Volume: 37 Issue: 31 Pages: 2687-2700

    • DOI

      10.1002/jcc.24494

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Omokage search: shape similarity search service for biomolecular structures in both the PDB and EMDB.2016

    • Author(s)
      Hirofumi Suzuki, Takeshi Kawabata, Haruki Nakamura
    • Journal Title

      Bioinformatics

      Volume: 32 Issue: 4 Pages: 619-620

    • DOI

      10.1093/bioinformatics/btv614

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Density functional study of molecular interactions in secondary structures of proteins2016

    • Author(s)
      Takano Y, Kusaka A, Nakamura H
    • Journal Title

      Biophysics and Physicobiology

      Volume: 13 Issue: 0 Pages: 27-35

    • DOI

      10.2142/biophysico.13.0_27

    • NAID

      130005126232

    • ISSN
      2189-4779
    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Development of Massive Multilevel Molecular Dynamics Simulation Program, Platypus (PLATform for dYnamic Protein Unified Simulation), for the Elucidation of Protein2016

    • Author(s)
      Takano Y, Nakata K, Yonezawa Y, Nakamura H
    • Journal Title

      Journal of Computational Chemistry

      Volume: 37 Issue: 12 Pages: 1125-1132

    • DOI

      10.1002/jcc.24318

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] A critical appraisal of the zero-multipole method: Structural, thermodynamic, dielectrid, and dynamical properties of a water system2016

    • Author(s)
      Wang H, Nakamura H, Fukuda I
    • Journal Title

      Journal of Chemical Physics

      Volume: 144 Issue: 11 Pages: 114503-114503

    • DOI

      10.1063/1.4943956

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] SMARCAD1 is an ATP-dependent stimulator of nucleosomal H2A acetylation via CBP, resulting in transcriptional regulation.2016

    • Author(s)
      Doiguchi M
    • Journal Title

      Sci. Rep.

      Volume: 6 Issue: 1 Pages: 20179-20179

    • DOI

      10.1038/srep20179

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Virtual-system coupled adaptive umbrella sampling to compute free-energy landscape for flexible molecular docking2015

    • Author(s)
      Higo J, Dasgupta B, Mashimo T, Kasahara K, Fukunishi Y, Nakamura H
    • Journal Title

      Journal of Computational Chemistry

      Volume: 36 Issue: 20 Pages: 1489-1501

    • DOI

      10.1002/jcc.23948

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Computational Study of Drug Binding Affinity to Influenza A Neuraminidase Using Smooth Reaction Path Generation (SRPG) Method2015

    • Author(s)
      Nguyen H, Tran T, Fukunishi Y, Higo J, Nakamura H, Le L
    • Journal Title

      Journal of Chemical Information and Modeling

      Volume: 55 Issue: 9 Pages: 1936-1943

    • DOI

      10.1021/acs.jcim.5b00319

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] A Selective G-Quadruplex DNA-Stabilizing Ligand Based on a Cyclic Naphthalene Diimide Derivative2015

    • Author(s)
      Md. Monirul Islam, Satoshi Fujii, Shinobu Sato, Tatsuo Okauchi & Shigeori Takenaka
    • Journal Title

      Molecules

      Volume: 20 Issue: 6 Pages: 10963-10979

    • DOI

      10.3390/molecules200610963

    • NAID

      120005756674

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] Thermodynamics and kinetic studies in the binding interaction of cyclic naphthalene diimide derivatives with double stranded DNAs2015

    • Author(s)
      Md. Monirul Islam, Satoshi Fujii, Shinobu Sato, Tatsuo Okauchi, Shigeori Takenaka
    • Journal Title

      Bioorganic & Medicinal Chemistry

      Volume: 23 Issue: 15 Pages: 4769-4776

    • DOI

      10.1016/j.bmc.2015.05.046

    • NAID

      120006332122

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Cooperative Binding of Ferrocenylnaphthalene Diimide Carrying β-Cyclodextrin Converts Double-Stranded DNA to a Rod-Like Structure2015

    • Author(s)
      Shinobu Sato, Yuta Umeda, Satoshi Fujii & Shigeori Takenaka
    • Journal Title

      Bioconjugate Chem.

      Volume: 26 Issue: 3 Pages: 379-382

    • DOI

      10.1021/bc500535n

    • NAID

      120005713351

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Dzip3 regulates developmental genes in mouse embryonic stem cells by reorganizing 3D chromatin conformation.2015

    • Author(s)
      Inoue D, Aihara H, Sato T, Mizusaki H, Doiguchi M, Higashi M, Imamura Y, Yoneda M, Miyanishi T, Fujii S, Okuda A, Nakagawa T, Ito T
    • Journal Title

      Scientific Reports

      Volume: 5 Issue: 1 Pages: 16567-16567

    • DOI

      10.1038/srep16567

    • NAID

      120006986837

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] Identification of diphtheria toxin R domain mutants with enhanced inhibitory activity against HB-EGF2015

    • Author(s)
      Suzuki K, Mizushima H, Abe H, Iwamoto R, Nakamura H, Mekada E
    • Journal Title

      J Biochem

      Volume: mvu079 Issue: 5 Pages: 331-343

    • DOI

      10.1093/jb/mvu079

    • NAID

      40020461422

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] High-resolution modeling of antibody structures by a combination of bioinformatics, expert knowledge, and molecular simulations.2014

    • Author(s)
      Hiroki Shirai, Kazuyoshi Ikeda, Kazuo Yamashita, Yuko Tsuchiya, Jamica Sarmiento, Shide Liang, Tatsuaki Morokata, Kenji Mizuguchi, Junichi Higo, Daron M. Standley, Haruki Nakamura
    • Journal Title

      Proteins

      Volume: 印刷中 Issue: 8 Pages: 1624-1635

    • DOI

      10.1002/prot.24591

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] The Zero-multipole summation method for estimating electrostatic interactions in molecular dynamics : analysis of the accuracy and application to liquid systems2014

    • Author(s)
      Fukuda I, Kamiya N, Nakamura H
    • Journal Title

      J. Chem. Phys

      Volume: 140 Issue: 19 Pages: 194307-194307

    • DOI

      10.1063/1.4875693

    • NAID

      120005596268

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Structure of the entire stalk region of the dynein motor domain2014

    • Author(s)
      Yosuke Nishikawa, Takuji Oyama, Narutoshi Kamiya, Takahide Kon, Yoko Y. Toyoshima, Haruki Nakamura, Genji Kurisu
    • Journal Title

      Journal of Molecular Biology

      Volume: 426 Issue: 19 Pages: 3232-3245

    • DOI

      10.1016/j.jmb.2014.06.023

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A Novel Approach of Dynamic Cross Correlation Analysis on Molecular Dynamics Simulations and its Application to Ets1 dimer–DNA Complex2014

    • Author(s)
      Kota Kasahara, Ikuo Fukuda, Haruki Nakamura
    • Journal Title

      PLoS One

      Volume: 9 (11) Issue: 11 Pages: e112419-e112419

    • DOI

      10.1371/journal.pone.0112419

    • NAID

      120005596267

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Design of tetraplex specific ligands: cyclic naphthalene diimide2014

    • Author(s)
      Yugo Esaki, Md. Monirul Islam, Satoshi Fujii, Shinobu Sato, Shigeori Takenaka
    • Journal Title

      Chemical Communications

      Volume: 50 Issue: 45 Pages: 5967-5969

    • DOI

      10.1039/c4cc01005a

    • NAID

      120005741791

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] A virtual-system coupled multicanonical molecular dynamics simulation : Principles and applications to free-energy landscape of protein-protein interaction with an all-atom model in explicit solvent2013

    • Author(s)
      J. Higo, K. Umezawa, H. Nakamura
    • Journal Title

      Journal of Chemical Physics

      Volume: 138 Issue: 18 Pages: 184106-184106

    • DOI

      10.1063/1.4803468

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] LigandBox: A database for 3D structures of chemical compounds2013

    • Author(s)
      Takeshi Kawabata, Yusuke Sugihara, Yoshifumi Fukunishi, Haruki Nakamura
    • Journal Title

      BIOPHYSICS

      Volume: 9 Issue: 0 Pages: 113-121

    • DOI

      10.2142/biophysics.9.113

    • NAID

      130003366038

    • ISSN
      1349-2942
    • Related Report
      2013 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Exhaustive comparison and classification of ligand-binding surfaces in proteins2013

    • Author(s)
      Murakami Y, Kinoshita K, Kinjo AR, Nakamura H
    • Journal Title

      Protein Science

      Volume: 22 Issue: 10 Pages: 1379-1391

    • DOI

      10.1002/pro.2329

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Molecular dynamics simulations of a double-stranded DNA in an explicit solvent model with zero-dipole summation method2013

    • Author(s)
      Arakawa T, Kamiya N, Nakamura H, Fukuda I
    • Journal Title

      PLoS ONE

      Volume: 8 Issue: 10 Pages: e76606-e76606

    • DOI

      10.1371/journal.pone.0076606

    • Related Report
      2013 Annual Research Report 2012 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Application of zero-dipole summation method to molecular dynamics2013

    • Author(s)
      Narutoshi Kamiya
    • Journal Title

      Chem. Phys. Lett.

      Volume: 568-569 Pages: 26-32

    • DOI

      10.1016/j.cplett.2013.03.014

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] NF-E2 p45 Activates Genes Involved in the Regulation of Platelet Function.2013

    • Author(s)
      Rie Fujita, Mariko Takayama-Tsujimoto, Hironori Satoh, Laura Gutiérrez, Hiroyuki Aburatani, Satoshi Fujii, Akinori Sarai, Emery H. Bresnick, Masayuki Yamamoto, Hozumi Motohashi
    • Journal Title

      Molecular and Cellular Biology

      Volume: 33 Pages: 2659-2670

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Simple and Accurate Scheme to Compute Electrostatic Interactions: Zero-dipole Summation Technique for Molecular System and Application to Bulk Water.2012

    • Author(s)
      Ikuo Fukuda, Narutoshi Kamiya, Yasushige Yonezawa, Haruki Nakamura
    • Journal Title

      Journal of Chemical Physics

      Volume: 137 Issue: 5 Pages: 54314-54314

    • DOI

      10.1063/1.4739789

    • NAID

      120005647641

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Non-Ewald methods : Theory and Applications to Molecular Systems2012

    • Author(s)
      Fukuda I, Nakamura H
    • Journal Title

      Biophysical Reviews

      Volume: 4 Issue: 3 Pages: 161-170

    • DOI

      10.1007/s12551-012-0089-4

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Presentation] ウェットとドライの真の融合を目指して2017

    • Author(s)
      藤井 聡
    • Organizer
      冬の若手ワークショップ2017
    • Place of Presentation
      一宮シーサイドオーツカ(千葉県、長生郡一宮町)
    • Year and Date
      2017-01-30
    • Related Report
      2016 Annual Research Report
  • [Presentation] 転写因子とヒストン修飾の関連性を提示するためのデータベース構築2017

    • Author(s)
      飯田 緑、藤井 聡
    • Organizer
      冬の若手ワークショップ2017
    • Place of Presentation
      一宮シーサイドオーツカ(千葉県、長生郡一宮町)
    • Year and Date
      2017-01-30
    • Related Report
      2016 Annual Research Report
  • [Presentation] Multi-modal Dynamic Cross Correlation (mDCC) 法の開発と転写因子- DNA 複合体における動的相関ネットワークの解析2017

    • Author(s)
      笠原 浩太
    • Organizer
      名古屋大学 IGER セミナー
    • Place of Presentation
      名古屋大学(愛知県、名古屋市)
    • Related Report
      2016 Annual Research Report
  • [Presentation] 天然変性領域による転写制御の分子機構2017

    • Author(s)
      笠原 浩太
    • Organizer
      第5回 関西4私大 生命科学シンポジウム
    • Place of Presentation
      関西学院会館光の間(兵庫県、西宮市)
    • Related Report
      2016 Annual Research Report
  • [Presentation] Flexible docking between cyclin-dependent kinase 2 and its inhibitor using multicanonical MD2016

    • Author(s)
      Gert-Jan Bekker, Narutoshi Kamiya, Mitsugu Araki, Yasushi Okuno, Haruki Nakamura
    • Organizer
      第54回日本生物物理学会年会
    • Place of Presentation
      つくば国際会議場(茨城県、つくば市)
    • Year and Date
      2016-11-25
    • Related Report
      2016 Annual Research Report
  • [Presentation] 分子シミュレーションにおける静電相互作用計算法:零多重極子法の理論と実際2016

    • Author(s)
      福田 育夫, Wang Han, 神谷 成敏, 笠原 浩太, 寺田 透, 櫻庭 俊, 中村 春木
    • Organizer
      第54回日本生物物理学会年会
    • Place of Presentation
      つくば国際会議場(茨城県、つくば市)
    • Year and Date
      2016-11-25
    • Related Report
      2016 Annual Research Report
  • [Presentation] Oct4の2つのDNA結合サブドメインを結ぶ柔軟なlinker領域の自由エネルギー地形2016

    • Author(s)
      速水 智教、高田 彰二、中村 春木、肥後 順一
    • Organizer
      第54回日本生物物理学会年会
    • Place of Presentation
      つくば国際会議場(茨城県、つくば市)
    • Year and Date
      2016-11-25
    • Related Report
      2016 Annual Research Report
  • [Presentation] 巨大生体分子の長時間 MD シミュレーションの開発と生体分子の構造機能相関の解明2016

    • Author(s)
      鷹野 優、Neetha Mohan、草鹿 あゆみ、川端 猛、笠原 浩太、真下 忠彰、神谷 成敏、中村 春木
    • Organizer
      第8回「学際計算科学による新たな知の発展・統合・創出」シンポジウム
    • Place of Presentation
      筑波大学計算科学研究センター(茨城県、つくば市)
    • Year and Date
      2016-10-17
    • Related Report
      2016 Annual Research Report
  • [Presentation] 公共ChIP-Seqデータの統合解析による転写制御の解析2016

    • Author(s)
      藤井 聡
    • Organizer
      転写サイクル合同班会議2016
    • Place of Presentation
      松島一の坊(宮城県宮城郡松島町)
    • Year and Date
      2016-09-05
    • Related Report
      2016 Annual Research Report
  • [Presentation] 転写産物とPolIIエンリッチメントプロファイリングによるDecapping exoribonuclease (Dom3z) の機能解析2016

    • Author(s)
      飯田 緑、磯部 智康、山口 雄輝、藤井 聡
    • Organizer
      転写サイクル合同班会議2016
    • Place of Presentation
      松島一の坊(宮城県宮城郡松島町)
    • Year and Date
      2016-09-05
    • Related Report
      2016 Annual Research Report
  • [Presentation] 計算・情報科学による 転写サイクルにおける情報変換機構の解明2016

    • Author(s)
      笠原 浩太、Neetha Mohan、中村 春木
    • Organizer
      転写サイクル合同班会議2016
    • Place of Presentation
      松島一の坊(宮城県宮城郡松島町)
    • Year and Date
      2016-09-05
    • Related Report
      2016 Annual Research Report
  • [Presentation] p53 C末端ドメインのアセチル化およびヒスチジンの荷電状態の変化がその立体構造集団に及ぼす影響2016

    • Author(s)
      飯田 慎仁, 牟田 寛弥, 後藤 祐児, 北條 裕信, 中村 春木, 肥後 順一
    • Organizer
      第16回日本蛋白質科学会年会
    • Place of Presentation
      福岡国際会議場(福岡県、福岡市)
    • Year and Date
      2016-06-07
    • Related Report
      2016 Annual Research Report
  • [Presentation] 天然変性領域の過渡的な相互作用による転写制御の分子機構2016

    • Author(s)
      笠原 浩太、椎名 政昭、肥後 順一、緒方 一博、中村 春木
    • Organizer
      第16回日本蛋白質科学会年会
    • Place of Presentation
      福岡国際会議場(福岡県、福岡市)
    • Year and Date
      2016-06-07
    • Related Report
      2016 Annual Research Report
  • [Presentation] Insights Derived from Molecular Dynamics Simulations into the Subunit Assembly and Clamp Motions of Thermococcus kodakarensis RNA Polymerase2016

    • Author(s)
      Neetha Mohan, Kota Kasahara, Akira Hirata, Haruki Nakamura
    • Organizer
      第16回日本蛋白質科学会年会
    • Place of Presentation
      福岡国際会議場(福岡県、福岡市)
    • Year and Date
      2016-06-07
    • Related Report
      2016 Annual Research Report
  • [Presentation] An efficient new methodology for path elucidation and binding free energy calculation2016

    • Author(s)
      Gert-Jan Bekker, Narutoshi Kamiya, Haruki Nakamura
    • Organizer
      第16回日本蛋白質科学会年会
    • Place of Presentation
      福岡国際会議場(福岡県、福岡市)
    • Year and Date
      2016-06-07
    • Related Report
      2016 Annual Research Report
  • [Presentation] BigData to Knowledge to Wisdom2016

    • Author(s)
      Haruki Nakamura
    • Organizer
      Data Sharing Symposium
    • Place of Presentation
      一橋講堂(東京)
    • Year and Date
      2016-02-29
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 公共ChIP-Seqデータの統合解析による協同的制御機構の解析2016

    • Author(s)
      藤井 聡
    • Organizer
      冬の若手ワークショップ2015
    • Place of Presentation
      山中湖畔荘 ホテル清渓(山梨県南都留郡)
    • Year and Date
      2016-02-04
    • Related Report
      2015 Annual Research Report
  • [Presentation] Decapping exoribonuclease(DOX:Dom3z)の転写制御における機能解析2016

    • Author(s)
      飯田 緑、磯部 智康、山口 雄輝、藤井 聡
    • Organizer
      冬の若手ワークショップ2015
    • Place of Presentation
      山中湖畔荘 ホテル清渓(山梨県南都留郡)
    • Year and Date
      2016-02-04
    • Related Report
      2015 Annual Research Report
  • [Presentation] Computational approaches to analyze and predict protein-protein interactions2016

    • Author(s)
      Haruki Nakamura
    • Organizer
      IPR International Workshop
    • Place of Presentation
      大阪大学蛋白質研究所 (大阪府)
    • Year and Date
      2016-02-02
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] New Methods for Structure Guided Drug Development2016

    • Author(s)
      Haruki Nakamura
    • Organizer
      JCUP VII
    • Place of Presentation
      大手町サンスカイルーム朝日生命大手町ビル(東京都、千代田区)
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Computational Approaches to Coupled Folding and Binding in Protein-Protein Interactions2016

    • Author(s)
      Haruki Nakamura
    • Organizer
      21st Biophysics Conference
    • Place of Presentation
      Hsinchu (Taiwan)
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Computational analysis on electrostatic properties of protein and Protein-Protein Interactions2016

    • Author(s)
      Haruki Nakamura
    • Organizer
      Asia Pacific Protein Association (APPA), IPR International Seminar
    • Place of Presentation
      大阪大学蛋白質研究所(大阪府、吹田市)
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] バイオインフォマティクスの世界へようこそ2016

    • Author(s)
      飯田 緑
    • Organizer
      第3回LaMer 特別講演会
    • Place of Presentation
      愛媛大学(愛媛県、松山市)
    • Related Report
      2016 Annual Research Report
  • [Presentation] Computational Approaches to Coupled Folding and Binding in Protein-Protein Interactions2016

    • Author(s)
      Haruki Nakamura
    • Organizer
      The 11th International Symposium of the Protein Society of Thailand
    • Place of Presentation
      Bangkok (Thailand)
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Computational Approaches to Protein Interactions2016

    • Author(s)
      Haruki Nakamura
    • Organizer
      Japan-Slovenia JSPS Bilateral scientific exchange
    • Place of Presentation
      Koper (Slovenia)
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Computational approach to find a specific interaction among many IDR relating fuzzy complexes2015

    • Author(s)
      Haruki Nakamura
    • Organizer
      International Symposium on Structure and Folding of Disease Related Proteins
    • Place of Presentation
      Seoul National University (韓国)
    • Year and Date
      2015-12-04
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] A specific interaction among many fuzzy complexes regulated by phosphorylation: Molecular simulation approach2015

    • Author(s)
      Haruki Nakamura
    • Organizer
      RSC/IPR Joint Symposium “Protein Structure and Function”
    • Place of Presentation
      Australian National University (Canberra)
    • Year and Date
      2015-11-14
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 転写因子Ets1天然変性領域のリン酸化によるDNA認識阻害メカニズムの検討2015

    • Author(s)
      笠原浩太、肥後順一、椎名政昭、緒方一博、中村春木
    • Organizer
      第53回日本生物物理学会年会
    • Place of Presentation
      金沢大学角間キャンパス(金沢市)
    • Year and Date
      2015-09-13
    • Related Report
      2015 Annual Research Report
  • [Presentation] EMDBとPDBデータの形状類似検索:Omokage検索2015

    • Author(s)
      鈴木博文, 川端猛, 中村春木
    • Organizer
      第53回日本生物物理学会年会
    • Place of Presentation
      金沢大学角間キャンパス(金沢市)
    • Year and Date
      2015-09-13
    • Related Report
      2015 Annual Research Report
  • [Presentation] ヘムの構造歪みが酸化還元電位に与える影響の計算科学的研究2015

    • Author(s)
      今田康博, 中村春木, 鷹野優
    • Organizer
      第53回日本生物物理学会年会
    • Place of Presentation
      金沢大学角間キャンパス(金沢市)
    • Year and Date
      2015-09-13
    • Related Report
      2015 Annual Research Report
  • [Presentation] 抗体CDR-H3ループ領域の立体構造予測2015

    • Author(s)
      西上博士, Gert-Jan Bekker, 神谷成敏, 肥後順一, 中村春木
    • Organizer
      第53回日本生物物理学会年会
    • Place of Presentation
      金沢大学角間キャンパス(金沢市)
    • Year and Date
      2015-09-13
    • Related Report
      2015 Annual Research Report
  • [Presentation] 天然変性領域であるp53C末端ドメインの構造と物性にアセチル化が及ぼす影響2015

    • Author(s)
      飯田慎仁, 北條裕信, 中村春木, 肥後順一
    • Organizer
      第53回日本生物物理学会年会
    • Place of Presentation
      金沢大学角間キャンパス(金沢市)
    • Year and Date
      2015-09-13
    • Related Report
      2015 Annual Research Report
  • [Presentation] On the convergence of binding free-energy landscape calculation by improved virtual-system coupled adaptive umbrella sampling2015

    • Author(s)
      Bhaskar Dasgupta, 肥後順一, 中村春木
    • Organizer
      第53回日本生物物理学会年会
    • Place of Presentation
      金沢大学角間キャンパス(金沢市)
    • Year and Date
      2015-09-13
    • Related Report
      2015 Annual Research Report
  • [Presentation] A novel method to determine the optimal unbinding path between receptor and ligand using advanced molecular dynamics simulation2015

    • Author(s)
      Gert-Jan Bekker, 神谷成敏, 中村春木
    • Organizer
      第53回日本生物物理学会年会
    • Place of Presentation
      金沢大学角間キャンパス(金沢市)
    • Year and Date
      2015-09-13
    • Related Report
      2015 Annual Research Report
  • [Presentation] 低解像度密度マップへの複数のサブユニットのあてはめ計算-実験情報による拘束の利用-2015

    • Author(s)
      川端猛, 鈴木博文, 中村春木
    • Organizer
      第53回日本生物物理学会年会
    • Place of Presentation
      金沢大学角間キャンパス(金沢市)
    • Year and Date
      2015-09-13
    • Related Report
      2015 Annual Research Report
  • [Presentation] Molecular Tailoring Approach法による蛋白質二次構造内に働く相互作用の量子化学的研究2015

    • Author(s)
      草鹿あゆみ, 中村春木, 鷹野優
    • Organizer
      第53回日本生物物理学会年会
    • Place of Presentation
      金沢大学角間キャンパス(金沢市)
    • Year and Date
      2015-09-13
    • Related Report
      2015 Annual Research Report
  • [Presentation] 分子シミュレーションにおける静電相互作用計算のための新規非エバルト法2015

    • Author(s)
      福田育夫, 神谷成敏, Han Wang, 笠原浩太、中村春木
    • Organizer
      第53回日本生物物理学会年会
    • Place of Presentation
      金沢大学角間キャンパス(金沢市)
    • Year and Date
      2015-09-13
    • Related Report
      2015 Annual Research Report
  • [Presentation] Interaction of two subunits of D/L hetero dimer with catalytic subunits in archaeal RNA polymerase: Insights from MD simulations2015

    • Author(s)
      Neetha Mohan, 笠原浩太、平田章、中村春木
    • Organizer
      第53回日本生物物理学会年会
    • Place of Presentation
      金沢大学角間キャンパス(金沢市)
    • Year and Date
      2015-09-13
    • Related Report
      2015 Annual Research Report
  • [Presentation] 分子シミュレーションから解き明かす転写因子Ets1のDNA結合調節機構2015

    • Author(s)
      笠原浩太、Neetha Mohan、肥後順一、福田育夫、中村春木
    • Organizer
      転写サイクル合同班会議2015
    • Place of Presentation
      ホテル暖香園(静岡県伊東市)
    • Year and Date
      2015-08-03
    • Related Report
      2015 Annual Research Report
  • [Presentation] 転写制御に関係するヒストン修飾パターンの解析2015

    • Author(s)
      藤井 聡、西山 晃、田村 智彦
    • Organizer
      転写サイクル合同班会議2015
    • Place of Presentation
      ホテル暖香園(静岡県伊東市)
    • Year and Date
      2015-08-03
    • Related Report
      2015 Annual Research Report
  • [Presentation] RNA polymerase IIのプロファイル解析2015

    • Author(s)
      飯田 緑、磯部 智康、山口 雄輝、藤井 聡
    • Organizer
      転写サイクル合同班会議2015
    • Place of Presentation
      ホテル暖香園(静岡県伊東市)
    • Year and Date
      2015-08-03
    • Related Report
      2015 Annual Research Report
  • [Presentation] Computational Approaches to Coupled Folding and Binding in Protein-Protein Interactions2015

    • Author(s)
      Haruki Nakamura
    • Organizer
      19th KPPS (Korean Peptide Protein Symposium) Symposium
    • Place of Presentation
      Resom Ocean Castle Resort, Korea
    • Year and Date
      2015-07-07
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] プール型shRNAシークエンス(shRNA-seq)スクリーニングデータ解析法の開発2015

    • Author(s)
      藤井 聡
    • Organizer
      NGS現場の会第四回研究会
    • Place of Presentation
      つくば国際会議場(茨城県つくば市)
    • Year and Date
      2015-07-01
    • Related Report
      2015 Annual Research Report
  • [Presentation] ヘムの構造歪みが酸化還元電位に与える影響の計算科学的研究2015

    • Author(s)
      今田康博, 中村春木, 鷹野優
    • Organizer
      第15回日本蛋白質科学会年会
    • Place of Presentation
      あわぎんホール(徳島市)
    • Year and Date
      2015-06-24
    • Related Report
      2015 Annual Research Report
  • [Presentation] p53蛋白質C末端天然変性領域の構造探索2015

    • Author(s)
      飯田慎仁, 神谷成敏, 北條裕信, 中村春木, 肥後順一
    • Organizer
      第15回日本蛋白質科学会年会
    • Place of Presentation
      あわぎんホール(徳島市)
    • Year and Date
      2015-06-24
    • Related Report
      2015 Annual Research Report
  • [Presentation] 転写因子Ets1とパートナー転写因子の協調的結合によるDNA結合活性制御機構の計算科学的検討2015

    • Author(s)
      笠原浩太, 福田育夫, 中村春木
    • Organizer
      第15回日本蛋白質科学会年会
    • Place of Presentation
      あわぎんホール(徳島市)
    • Year and Date
      2015-06-24
    • Related Report
      2015 Annual Research Report
  • [Presentation] FRET法とRAMD法を用いた核内受容体PPARγのリガンド結合に関する実験・理論的研究2015

    • Author(s)
      神谷成敏, Gert-Jan Bekker, 白木琢磨, 中村春木
    • Organizer
      第15回日本蛋白質科学会年会
    • Place of Presentation
      あわぎんホール(徳島市)
    • Year and Date
      2015-06-24
    • Related Report
      2015 Annual Research Report
  • [Presentation] Molecular Tailoring Approachによるタンパク質の二次構造に働く相互作用の量子化学的解析2015

    • Author(s)
      鷹野優, 草鹿あゆみ, 中村春木
    • Organizer
      第15回日本蛋白質科学会年会
    • Place of Presentation
      あわぎんホール(徳島市)
    • Year and Date
      2015-06-24
    • Related Report
      2015 Annual Research Report
  • [Presentation] HOMCOSサーバを用いた複合体立体構造の進化的保存性の解析2015

    • Author(s)
      川端猛, 中村春木
    • Organizer
      第15回日本蛋白質科学会年会
    • Place of Presentation
      あわぎんホール(徳島市)
    • Year and Date
      2015-06-24
    • Related Report
      2015 Annual Research Report
  • [Presentation] EMDBとPDBを対象とした形状類似性検索:Omokage検索2015

    • Author(s)
      鈴木博文, 川端猛, 中村春木
    • Organizer
      第15回日本蛋白質科学会年会
    • Place of Presentation
      あわぎんホール(徳島市)
    • Year and Date
      2015-06-24
    • Related Report
      2015 Annual Research Report
  • [Presentation] Prediction of protein-protein and protein-ligand interactions, and application to drug discovery2015

    • Author(s)
      Haruki Nakamura
    • Organizer
      The 9th Asian Biophysics Association Symposium (ABA2015
    • Place of Presentation
      Hangzhou, China
    • Year and Date
      2015-05-10
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Computational analysis on electrostatic properties of proteins and their assembly.2015

    • Author(s)
      Haruki Nakamura
    • Organizer
      The first trilateral workshop for frontier protein studies
    • Place of Presentation
      Peking University, China
    • Year and Date
      2015-04-23
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 転写因子Ets1の天然変性領域によるDNA認識調節メカニズムに関する計算化学的検討2015

    • Author(s)
      笠原浩太
    • Organizer
      第3回天然変性蛋白質計算科学セミナー
    • Place of Presentation
      御殿場高原時之栖、御殿場市
    • Year and Date
      2015-03-11
    • Related Report
      2014 Annual Research Report
  • [Presentation] PDBnet: Integration of Structural and Biochemical Protein-Protein Interaction Network2014

    • Author(s)
      Satoshi Fujii
    • Organizer
      GIW / ISCB-Asia 2014
    • Place of Presentation
      東京国際交流館、東京台場
    • Year and Date
      2014-12-15 – 2014-12-17
    • Related Report
      2014 Annual Research Report
  • [Presentation] Significance Analysis of shRNA-seq Applied to the Pooled Lentiviral shRNA Expression Libraries2014

    • Author(s)
      Midori Iida, Shunpei Tateno, Yuki Yamaguchi, Satoshi Fujii
    • Organizer
      GIW / ISCB-Asia 2014
    • Place of Presentation
      東京国際交流館、東京台場
    • Year and Date
      2014-12-15 – 2014-12-17
    • Related Report
      2014 Annual Research Report
  • [Presentation] 遺伝子発現データに基づく大腸癌サブタイプ探索~教師なし学習法~2014

    • Author(s)
      原田佳織、山﨑敏正、藤井 聡、飯田 緑、青柳一彦、山田康秀、佐々木博己
    • Organizer
      第21回日本生物工学会九州支部 熊本大会
    • Place of Presentation
      熊本大学、熊本市
    • Year and Date
      2014-12-06
    • Related Report
      2014 Annual Research Report
  • [Presentation] 遺伝子発現データ解析による食道癌患者サブタイプ分類2014

    • Author(s)
      村上絢夏、藤井 聡、飯田 緑、山﨑敏正、青柳一彦、佐々木博己
    • Organizer
      第21回日本生物工学会九州支部 熊本大会
    • Place of Presentation
      熊本大学、熊本市
    • Year and Date
      2014-12-06
    • Related Report
      2014 Annual Research Report
  • [Presentation] DNA structural study under ethanol/water mixture based on molecular dynamics simulations2014

    • Author(s)
      Satoshi Fujii, Hidetoshi Kono
    • Organizer
      第41回 国際核酸化学シンポジウム
    • Place of Presentation
      北九州国際会議場、福岡市
    • Year and Date
      2014-11-05 – 2014-11-07
    • Related Report
      2014 Annual Research Report
  • [Presentation] Zero-dipole summation法を用いたエンハンソソーム制御メカニズムの分子動力学的解析2014

    • Author(s)
      笠原浩太、福田育夫
    • Organizer
      第1回「京」を中核とするHPCIシステム利用研究課題成果報告会
    • Place of Presentation
      コクヨホール、東京品川
    • Year and Date
      2014-10-31
    • Related Report
      2014 Annual Research Report
  • [Presentation] 分子動力学シミュレーション解析のためのMulti-modal Dynamic Cross Correlation法の開発と応用2014

    • Author(s)
      笠原浩太、福田育夫、中村春木
    • Organizer
      第3回生命医薬情報学連合大会
    • Place of Presentation
      仙台国際センター、仙台市
    • Year and Date
      2014-10-02 – 2014-10-04
    • Related Report
      2014 Annual Research Report
  • [Presentation] タンパク質構造情報による相互作用情報の統合2014

    • Author(s)
      藤井 聡
    • Organizer
      第3回生命医薬情報学連合大会
    • Place of Presentation
      仙台国際センター、仙台市
    • Year and Date
      2014-10-02 – 2014-10-04
    • Related Report
      2014 Annual Research Report
  • [Presentation] Cellecta社製プール型レンチウイルスshRNAライブラリー を用いたスクリーニングデータの解析法の開発2014

    • Author(s)
      飯田緑、舘野峻平、山口雄輝、藤井聡
    • Organizer
      第3回生命医薬情報学連合大会
    • Place of Presentation
      仙台国際センター、仙台市
    • Year and Date
      2014-10-02 – 2014-10-04
    • Related Report
      2014 Annual Research Report
  • [Presentation] Contact number diffusion model for the normal mode analysis of protein structure2014

    • Author(s)
      Bhaskar Dasgupta, Kota Kasahara, Narutoshi Kamiya, Haruki Nakamura, Akira Kinjo
    • 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
    • Year and Date
      2014-09-26
    • Related Report
      2014 Annual Research Report
  • [Presentation] Free-energy landscape of C-terminal negative regulatory domain of p532014

    • Author(s)
      Shinji Iida, Haruki Nakamura, Junini Higo
    • 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
    • Year and Date
      2014-09-25
    • Related Report
      2014 Annual Research Report
  • [Presentation] Elastic properties of dynein motor domain obatined from all-atom molecular dynamics simulations in explicit water2014

    • Author(s)
      Narutoshi Kamiya, Tadaaki Mashimo, Yu Takano, Takahide Kon, Genji Kurisu, Haruki Nakamura
    • 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
    • Year and Date
      2014-09-25
    • Related Report
      2014 Annual Research Report
  • [Presentation] Molecular dynamics study on cooperative binding of Ets1 and partner transcription factors on regulatory elements2014

    • Author(s)
      Kota Kasahara, Ikuo Fukuda, Haruki Nakamura
    • 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
    • Year and Date
      2014-09-25
    • Related Report
      2014 Annual Research Report
  • [Presentation] A new non-Ewald scheme for molecular dynamics simulation and its application to a free energy landscape for protein-protein interaction.2014

    • Author(s)
      Haruki Nakamura
    • Organizer
      2nd International Conference on Computational Science and Engineering (ICCSE 2014)
    • Place of Presentation
      Ho Chi Minh, Vietnam
    • Year and Date
      2014-08-23
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] 共用スパコンを用いた分子動力学シミュレーション研究2014

    • Author(s)
      笠原浩太
    • Organizer
      国立遺伝学研究所スーパーコンピュータユーザ会
    • Place of Presentation
      国立遺伝学研究所、三島市
    • Year and Date
      2014-07-22
    • Related Report
      2014 Annual Research Report
  • [Presentation] Free-energy landscape of the C-terminal negative regulatory domain of p532014

    • Author(s)
      Sinji Iida, Haruki Nakamura, Junichi Higo
    • Organizer
      第14回日本蛋白質科学会年会
    • Place of Presentation
      ワークピア横浜、横浜市
    • Year and Date
      2014-06-25
    • Related Report
      2014 Annual Research Report
  • [Presentation] 分子動力学法に基づいた新しい動的相関解析手法の開発と転写因子Ets-1-DNA結合機構解析への応用2014

    • Author(s)
      笠原浩太、福田育夫、中村春木
    • Organizer
      第14回日本蛋白質科学会年会
    • Place of Presentation
      ワークピア横浜、横浜市
    • Year and Date
      2014-06-25
    • Related Report
      2014 Annual Research Report
  • [Presentation] New Non-Ewald Scheme for Molecular Dynamics Simulation and Application to Free Energy Calculation2014

    • Author(s)
      Haruki Nakamura
    • Organizer
      Bioinformatics in Torun 2014 (BIT14)
    • Place of Presentation
      Torun, Poland
    • Year and Date
      2014-06-12
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] New Approach to Electrostatic Properties of Proteins and Protein-Protein Interactions2014

    • Author(s)
      Haruki Nakamura
    • Organizer
      The 4th Asia Pacific Protein Association (APPA 2014) (Plenary Lecture)
    • Place of Presentation
      ICC Jeju, Korea
    • Year and Date
      2014-05-18
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] Molecular dynamics study on enhancer recognitions by cooperative binding of Ets1 and partner transcription factors2014

    • Author(s)
      Kota Kasahara, Ikuo Fukuda, Haruki Nakamura
    • Organizer
      The 4th Asia Pacific Protein Association (APPA 2014)
    • Place of Presentation
      ICC Jeju, Korea
    • Year and Date
      2014-05-18
    • Related Report
      2014 Annual Research Report
  • [Presentation] Transcriptome Analysis of Red Seabream (Pagrus major) Embryos Treated with 2,3,7,8-Tetrachlorodibenzo-p-Dioxin (TCDD)2014

    • Author(s)
      M. Iida, S. Fujii, M. Uchida, H. Nakamura, Y. Kagami, S.M. Bak, E.Y. Kim, Y. Shima, H. Iwata
    • Organizer
      Society of Toxicology
    • Place of Presentation
      Phoenix Convention Center, Arizona, USA
    • Year and Date
      2014-03-23 – 2014-03-27
    • Related Report
      2013 Annual Research Report
  • [Presentation] 複数のChIP-Seqデータの統合解析手法の検討2014

    • Author(s)
      藤井 聡、西山 晃、田村 智彦
    • Organizer
      冬の若手ワークショップ 2014
    • Place of Presentation
      舌切雀のお宿 磯部ガーデン(軽井沢東 磯部温泉)
    • Year and Date
      2014-01-30 – 2014-02-01
    • Related Report
      2013 Annual Research Report
  • [Presentation] 転写因子Ets1のDNA結合制御に関する分子シミュレーション研究2014

    • Author(s)
      笠原 浩太,福田 育夫,中村 春木
    • Organizer
      冬の若手ワークショップ 2014
    • Place of Presentation
      舌切雀のお宿 磯部ガーデン(軽井沢東 磯部温泉)
    • Year and Date
      2014-01-30 – 2014-02-01
    • Related Report
      2013 Annual Research Report
  • [Presentation] Cellecta社製プール型レンチウイルスshRNAライブラリーを用いたスクリーニングデータ解析法の検討2014

    • Author(s)
      飯田 緑, 舘野 峻平, 山口 雄輝, 藤井 聡
    • Organizer
      冬の若手ワークショップ 2014
    • Place of Presentation
      舌切雀のお宿 磯部ガーデン(軽井沢東 磯部温泉)
    • Year and Date
      2014-01-30 – 2014-02-01
    • Related Report
      2013 Annual Research Report
  • [Presentation] Computational Protein Science: Structural Bioinformatics and Molecular Simulations2013

    • Author(s)
      Haruki Nakamura
    • Organizer
      CDAST symposium
    • Place of Presentation
      Jember University, Indonesia
    • Year and Date
      2013-12-14
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] TCDD曝露したマダイ胚のトランスクリプトーム解析2013

    • Author(s)
      飯田 緑, 藤井 聡, 内田 雅也, 中村 浩, 鏡 良弘, Bak, Su-Min, 金 恩英, 島 康洋, 岩田久人
    • Organizer
      日本内分泌撹乱化学物質学会
    • Place of Presentation
      東京大学
    • Year and Date
      2013-12-12 – 2013-12-13
    • Related Report
      2013 Annual Research Report
  • [Presentation] New Approaches to Dynamic Properties of Proteins and their Applications to Drug Discover of GPCR.2013

    • Author(s)
      Haruki Nakamura
    • Organizer
      CADD’13
    • Place of Presentation
      Institut Teknologi Bandung, Indonesia
    • Year and Date
      2013-12-12
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] PDBnet: Integration of Structural and Biochemical Information into Protein Interaction Network.2013

    • Author(s)
      Satoshi Fujii, Yuji Kawakami, Satoshi komori, Akinori Sarai
    • Organizer
      第36回日本分子生物学会年会
    • Place of Presentation
      神戸国際会議場(神戸市)
    • Year and Date
      2013-12-03 – 2013-12-06
    • Related Report
      2013 Annual Research Report
  • [Presentation] Zero-dipole summation method for evaluating eletrostatic interaction in molecular simulation of biomolecular system.2013

    • Author(s)
      Ikuo Fukuda, Narutoshi Kamiya, Haruki Nakamura
    • Organizer
      第51回日本生物物理学会年会
    • Place of Presentation
      国立京都国際会館(京都市)
    • Year and Date
      2013-10-28 – 2013-10-30
    • Related Report
      2013 Annual Research Report
  • [Presentation] Molecular dynamics study on ion conduction mechanisms of a voltage-sensitive potassium channel2013

    • Author(s)
      Kota Kasahara, Matsuyuki Shirota, Toshiyuki Saito, Hiroko Kondo, Kengo Kinoshita
    • Organizer
      第51回日本生物物理学会年会
    • Place of Presentation
      国立京都国際会館(京都市)
    • Year and Date
      2013-10-28 – 2013-10-30
    • Related Report
      2013 Annual Research Report 2012 Annual Research Report
  • [Presentation] 分子動力学法を用いた転写因子アロステリック制御機構の検討2013

    • Author(s)
      笠原 浩太
    • Organizer
      計算タンパク質科学研究会
    • Place of Presentation
      鳴子観光ホテル(宮城県)
    • Year and Date
      2013-09-18 – 2013-09-20
    • Related Report
      2013 Annual Research Report
  • [Presentation] ゲノム情報(1D)から蛋白質の動的構造情報(4D)へ2013

    • Author(s)
      中村 春木
    • Organizer
      日本学術会議公開シンポジウム
    • Place of Presentation
      日本学術会議講堂(東京)
    • Year and Date
      2013-09-17
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] Gene Expression Changes Exposed to 2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) in Early Developmental Stage Embryos of Red Seabream (Pagrus major)2013

    • Author(s)
      M. Iida, Y. Murakami, Y. Shima, H. Nakamura, Y. Kagami, S. Fujii, A. Srai, H. Iwata
    • Organizer
      転写サイクル合同班会議
    • Place of Presentation
      ホテルおかだ(箱根湯本温泉)
    • Year and Date
      2013-08-05 – 2013-08-07
    • Related Report
      2013 Annual Research Report
  • [Presentation] All-atom molecular dynamics simulations of dynein motor domain in explicit water2013

    • Author(s)
      Narutoshi Kamiya, Tadaaki Mashimo, Yu Takano, Takahide Kon, Genji Kurisu, Haruki Nakamura
    • Organizer
      Protein Society the 27th Annual Symposium
    • Place of Presentation
      Boston Marriott, Copley Place, Boston, USA
    • Year and Date
      2013-07-20 – 2013-07-23
    • Related Report
      2013 Annual Research Report
  • [Presentation] GIANT: a web- server for analyzing protein-small ligand interactions based on statistically preferred patterns of atomic contacts2013

    • Author(s)
      Kota Kasahara, Kengo Kinoshita
    • Organizer
      ISMB/ECCB 2013
    • Place of Presentation
      ICC Berlin, Berlin, Germany
    • Year and Date
      2013-07-18 – 2013-07-25
    • Related Report
      2013 Annual Research Report
  • [Presentation] The zero-dipole summation method and its application to molecular simulation with homogenous and inhomogeneous systems2013

    • Author(s)
      Ikuo Fukuda, Narutoshi Kamiya, Kota Kasahara, Haruki Nakamura
    • Organizer
      The 12th Asia Pacific Physics Conference (APPC12)
    • Place of Presentation
      幕張メッセ(千葉市) 大手町サンスカイルーム(東京)
    • Year and Date
      2013-07-15 – 2013-07-16
    • Related Report
      2013 Annual Research Report
  • [Presentation] Prediction of Protein-Protein Interactions: Structural Approaches.2013

    • Author(s)
      Haruki Nakamura
    • Organizer
      The 2nd HD Physiology International Symposium
    • Place of Presentation
      丸の内MY PLAZAホール(東京)
    • Year and Date
      2013-06-28
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] All-atomic molecular dynamics simulations of dynein motor domain in explicit water2013

    • Author(s)
      Narutoshi Kamiya, Tadaaki Mashimo, Yu Takano, Takahide Kon, Genji Kurisu, Haruki Nakamura
    • 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)
    • Year and Date
      2013-06-12 – 2013-06-14
    • Related Report
      2013 Annual Research Report 2012 Annual Research Report
  • [Presentation] GIANT: a database for pattern analysis of protein-small ligand atomic contacts2013

    • Author(s)
      Kota Kasahara, Kengo Kinoshita
    • 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)
    • Year and Date
      2013-06-12 – 2013-06-14
    • Related Report
      2013 Annual Research Report 2012 Annual Research Report
  • [Presentation] Measuring similarity of binding modes between 3D structures of protein–small ligand complexes.2013

    • Author(s)
      笠原 浩太
    • Organizer
      JCUP IV
    • Place of Presentation
      大手町サンスカイルーム(東京)
    • Year and Date
      2013-06-06 – 2013-06-07
    • Related Report
      2013 Annual Research Report
  • [Presentation] Measuring similarity of binding modes between 3D structures of protein–small ligand complexes2013

    • Author(s)
      笠原浩太
    • Organizer
      JCUP IV
    • Place of Presentation
      大手町サンスカイルーム(東京)
    • Related Report
      2012 Annual Research Report
  • [Presentation] The zero-dipole summation method and its application to molecular simulation with homogenous and inhomogeneous systems2013

    • Author(s)
      Ikuo Fukuda, Narutoshi Kamiya, Kota Kasahara, Haruki Nakamura
    • Organizer
      The 12th Asia Pacific Physics Conference (APPC12)
    • Place of Presentation
      幕張メッセ(千葉市)
    • Related Report
      2012 Annual Research Report
  • [Presentation] GIANT: a web-server for analyzing protein–small ligand interactions based on statistically preferred patterns of atomic contacts2013

    • Author(s)
      Kota Kasahara, Kengo Kinoshita
    • Organizer
      ISMB/ECCB 2013
    • Place of Presentation
      ICC Berlin, Berlin, Germany
    • Related Report
      2012 Annual Research Report
  • [Presentation] All-atom molecular dynamics simulations of dynein motor domain in explicit water2013

    • Author(s)
      Narutoshi Kamiya, Tadaaki Mashimo, Yu Takano, Takahide Kon, Genji Kurisu, Haruki Nakamura
    • Organizer
      Protein Society the 27th Annual Symposium
    • Place of Presentation
      Boston(USA)
    • Related Report
      2012 Annual Research Report
  • [Presentation] Zero-dipole summation method for evaluating eletrostatic interaction in molecular simulation of biomolecular system2013

    • Author(s)
      Ikuo Fukuda, Narutoshi Kamiya, Haruki Nakamura
    • Organizer
      第51回日本生物物理学会年会
    • Place of Presentation
      国立京都国際会館(京都市)
    • Related Report
      2012 Annual Research Report
  • [Presentation] Ion distribution in the EcoRV(restriction enzyme)-DNA complexcalculated by using 3D-RISM2012

    • Author(s)
      J.Yasuniwa, Y. Maruyama, N. Yoshida, A. Sarai, F. Hirata, M. Irisa
    • Organizer
      Foundations of Molecular Modeling and Simulation
    • Place of Presentation
      Mt. Hood, Oregon, USA
    • Related Report
      2012 Annual Research Report
  • [Presentation] A New Method for Evaluating the Specificity of Indirect Readout in Protein-DNA Recognition2012

    • Author(s)
      S. Yamasaki, T. Terada, H. Kono, K. Shimizu, A. Sarai
    • Organizer
      European Conference on Computational Biology
    • Place of Presentation
      Basel, Switzerland
    • Related Report
      2012 Annual Research Report
  • [Presentation] The influence of solvent condition on DNA structures studied by molecular dynamics simulations2012

    • Author(s)
      Satoshi Fujii, Hidetoshi Kono, Akinori Sarai
    • Organizer
      第50回日本生物物理学会年会
    • Place of Presentation
      名古屋大学
    • Related Report
      2012 Annual Research Report
  • [Presentation] Molecular Dynamics Simulations of Ets1-DNA complexes using Zero-Dipole Summation Method2012

    • Author(s)
      Takamasa Arakawa, Masaaki Shiina, Kazuhiro Ogata, Narutoshi Kamiya, Ikuo Fukuda, Haruki Nakamura
    • Organizer
      第50回日本生物物理学会年会
    • Place of Presentation
      名古屋大学
    • Related Report
      2012 Annual Research Report
  • [Presentation] Analysis of Transcriptional Regulation Network of Yeast2012

    • Author(s)
      Kazumasa Yada, Satoshi Fujii, Akinori Sarai
    • Organizer
      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
      2012 Annual Research Report
  • [Presentation] A simple non-Ewald scheme: the zero-dipole summation method and its application to molecular systems2012

    • Author(s)
      Ikuo Fukuda, Narutoshi Kamiya, Takamasa Arakawa, Haruki Nakamura
    • Organizer
      Conference on Computational Physics (CCP2012)
    • Place of Presentation
      ニチイ学館・神戸ポートアイランドセンター
    • Related Report
      2012 Annual Research Report
  • [Presentation] 3D-RISMを用いた酵素-DNA 複合体中の水和水分布計算2012

    • Author(s)
      本松良太, 安庭潤治, 丸山豊, 吉田紀生, 皿井明倫, 平田文男, 入佐正幸
    • Organizer
      第35回溶液化学シンポジウム
    • Place of Presentation
      早稲田大学(東京)
    • Related Report
      2012 Annual Research Report
  • [Presentation] Prediction of protein-protein complex structures

    • Author(s)
      Haruki Nakamura
    • Organizer
      International Conference on Biomolecular Forms and Functions
    • Place of Presentation
      Indian Institute of Science Bangalore, India
    • Related Report
      2012 Annual Research Report
    • Invited
  • [Presentation] A new non-Ewald scheme: The zero-dipole summation method and its applications to molecular dynamics simulations for homogeneous and inhomogeneous biomolecular systems

    • Author(s)
      Haruki Nakamura
    • Organizer
      National Symposium on Frontiers of Biophysics, Biotechnology & Bioinformatics and 37'th Annual Meeting of Indian Biophysical Society
    • Place of Presentation
      University of Mumbai, India
    • Related Report
      2012 Annual Research Report
    • Invited
  • [Presentation] A simple non-Ewald scheme for calculating electrostatic interactions of charged particle systems: the zero-dipole summation method and the application to molecular systems

    • Author(s)
      Ikuo Fukuda, Narutoshi Kamiya, Takamasa Arakawa, Tadaaki Mashimo, Yu Takano, Haruki Nakamura
    • Organizer
      2013年ハイパフォーマンスコンピューティングと計算科学シンポジウム
    • Place of Presentation
      東京工業大学 蔵前会館
    • Related Report
      2012 Annual Research Report
  • [Presentation] GPU-accelerated calculation of electrostatic interactions with zero-dipole summation method

    • Author(s)
      Tadaaki Mashimo, Yoshifumi Fukunishi, Ikuo Fukuda, Narutoshi Kamiya, Yu Takano, Haruki Nakamura
    • Organizer
      2013年ハイパフォーマンスコンピューティングと計算科学シンポジウム
    • Place of Presentation
      東京工業大学 蔵前会館
    • Related Report
      2012 Annual Research Report
  • [Presentation] Computational Prediction and Analysis of Protein-Protein Interactions: Qualitative and Quantitative Approaches

    • Author(s)
      Haruki Nakamura
    • Organizer
      Special Seminar at Academia Sinica
    • Place of Presentation
      Academia Sinica, Shanghai
    • Related Report
      2012 Annual Research Report
    • Invited
  • [Presentation] 生命科学における情報科学・計算科学

    • Author(s)
      中村春木
    • Organizer
      第6回三大学連携シンポジウム
    • Place of Presentation
      神戸大学統合研究拠点
    • Related Report
      2012 Annual Research Report
    • Invited
  • [Presentation] 分子シミュレーションにおける静電相互作用計算法について: Ewald, Non-Ewald, and Zero-dipole summation

    • Author(s)
      福田育夫
    • Organizer
      京阪奈計算生物物理セミナー
    • Place of Presentation
      京都大学理学部
    • Related Report
      2012 Annual Research Report
    • Invited
  • [Book] 生命のメカニズム - 美しいイメージで学ぶ構造生命科学入門 -2015

    • Author(s)
      中村春木(監訳)、工藤高裕、西川建、中村春木(訳)
    • Total Pages
      168
    • Publisher
      シナジー
    • Related Report
      2014 Annual Research Report
  • [Book] 見てわかる構造生命科学 - 生命科学研究へのタンパク質構造の利用 -2014

    • Author(s)
      中村春木(編)、中村春木他9名
    • Total Pages
      326
    • Publisher
      化学同人
    • Related Report
      2014 Annual Research Report
  • [Book] 生命科学から創薬へのイノベーション2014

    • Author(s)
      米田悦啓、堤康央、石井健(編)、中村春木他45名
    • Total Pages
      202
    • Publisher
      南山堂
    • Related Report
      2014 Annual Research Report
  • [Book] Biomolecular Forms and Functions: A Celebration of 50 years of the Ramachandran Map(Eds. Manju Bansal & N. Srinivasan)2013

    • Author(s)
      Kanamori E., Murakami Y., Sarmiento J., Liang S., Standley D. M., Shirota M., Kinoshita K., Tsuchiya Y., Higo J., Nakamura H.
    • Total Pages
      502
    • Publisher
      World Scientific Publishing
    • Related Report
      2012 Annual Research Report
  • [Remarks] 本新学術研究の公式webページ

    • URL

      http://transcriptioncycle.org

    • Related Report
      2015 Annual Research Report
  • [Remarks] Trancription Factor Annotation Tool

    • URL

      http://dna00.bio.kyutech.ac.jp/tfanno/

    • Related Report
      2015 Annual Research Report 2014 Annual Research Report
  • [Remarks] ChIP-Seqデータ解析トレーニングワークショップ

    • URL

      http://dna00.bio.kyutech.ac.jp/chipseqTW/program.html

    • Related Report
      2015 Annual Research Report 2014 Annual Research Report
  • [Remarks] 転写制御ポータル

    • URL

      http://www.abren.net/tfportal/new/

    • Related Report
      2013 Annual Research Report
  • [Remarks] 新学術領域研究「転写サイクル」

    • URL

      http://transcriptioncycle.org

    • Related Report
      2012 Annual Research Report
  • [Remarks] 転写制御ポータル

    • URL

      http://www.abren.net/tfportal/new/

    • Related Report
      2012 Annual Research Report

URL: 

Published: 2012-11-27   Modified: 2019-07-29  

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