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Quantitative computational and informatics studies on protein-protein interaction systems based on their dynamic structures

Research Project

Project/Area Number 23370071
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Research Field Biophysics
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) KINJO Akira R  大阪大学, たんぱく質研究所, 准教授 (30370117)
Co-Investigator(Renkei-kenkyūsha) HIGO Junichi  大阪大学, たんぱく質研究所, 特任研究員 (80265719)
KAMIYA Narutoshi  大阪大学, たんぱく質研究所, 特任研究員 (80420462)
YONEZAWA Yasushige  近畿大学, 先端技術総合研究所, 教授 (40248753)
Project Period (FY) 2011-04-01 – 2014-03-31
Project Status Completed (Fiscal Year 2013)
Budget Amount *help
¥19,760,000 (Direct Cost: ¥15,200,000、Indirect Cost: ¥4,560,000)
Fiscal Year 2013: ¥6,890,000 (Direct Cost: ¥5,300,000、Indirect Cost: ¥1,590,000)
Fiscal Year 2012: ¥6,890,000 (Direct Cost: ¥5,300,000、Indirect Cost: ¥1,590,000)
Fiscal Year 2011: ¥5,980,000 (Direct Cost: ¥4,600,000、Indirect Cost: ¥1,380,000)
Keywords構造・機能予測 / 分子シミュレーション / 蛋白質 / プロテオーム / 蛋白質間相互作用
Research Abstract

We have newly developed the V-McMD method, performing much more effective enhanced sampling than before. This method has been combined with our new non-Ewald method for rapid molecular dynamics simulations for the periodic system, so that the quantitative analysis for the stability of the protein dimer formation was made based on the free energy landscape for the molecular system, where the backbone and the side-chain conformations change upon binding. In addition, the local structures and molecular surfaces of the protein interfaces were investigated exhaustively, and many common patches are found to be shared in proteins across the different folds. The common structural motifs were identified, and the composite motifs, which are defined as the combination of those structural motifs, correspond well with the molecular functions of proteins.

Report

(4 results)
  • 2013 Annual Research Report   Final Research Report ( PDF )
  • 2012 Annual Research Report
  • 2011 Annual Research Report
  • Research Products

    (77 results)

All 2014 2013 2012 2011 Other

All Journal Article (25 results) (of which Peer Reviewed: 25 results,  Open Access: 5 results) Presentation (49 results) (of which Invited: 27 results) Book (2 results) Remarks (1 results)

  • [Journal Article] Rigid-body motions of interacting proteins dominate multi-specific binding of Ubiquitin in a shape-dependent manner2014

    • Author(s)
      Dasgupta B, Nakamura H, Kinjo AR
    • Journal Title

      Proteins

      Volume: 82 Issue: 1 Pages: 77-89

    • DOI

      10.1002/prot.24371

    • Related Report
      2013 Annual Research Report 2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Blind prediction of interfacial water positions in CAPRI2014

    • Author(s)
      Lensink MF, et al
    • Journal Title

      Proteins

      Volume: 82 Issue: 4 Pages: 620-632

    • DOI

      10.1002/prot.24439

    • Related Report
      2013 Annual Research Report 2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Specific non-local interactions are not necessary for recovering native protein dynamics2014

    • Author(s)
      Dasgupta B, Kasahara K, Kamiya N, Nakamura H, Kinjo AR
    • Journal Title

      PLoS ONE

      Volume: 9 Issue: 3 Pages: e91347-e91347

    • DOI

      10.1371/journal.pone.0091347

    • Related Report
      2013 Annual Research Report 2013 Final Research Report
    • Peer Reviewed
  • [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
      2013 Final 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
      2013 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
      2013 Final Research Report 2011 Annual Research Report
    • Peer Reviewed
  • [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 Final 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 Final Research Report 2012 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 Final Research Report 2012 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Molecular Dynamics Simulations Accelerated by GPU for Biological Macromolecules with a Non-Ewald Scheme for Electrostatic Interactions2013

    • Author(s)
      Mashimo T, Fukunishi Y, Kamiya N, Takano Y, Fukuda I, Nakamura H
    • Journal Title

      J. Chem. Theory Comput

      Volume: 9 Issue: 12 Pages: 5599-5609

    • DOI

      10.1021/ct400342e

    • NAID

      120005604144

    • Related Report
      2013 Annual Research Report 2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Mutational and Structural Analyses of Caldanaerobius polysaccharolyticus Man5B Reveal Novel Active Site Residues for Family 5 Glycoside Hydrolases2013

    • Author(s)
      Takuji Oyama, George E Schmitz, Dylan Dodd, Yejun Han, Alanna Burnett, Naoko Nagasawa, Roderick I Mackie, Haruki Nakamura, Kosuke Morikawa, & Isaac Cann
    • Journal Title

      PLoS ONE.

      Volume: 8 Issue: 11 Pages: e80448-e80448

    • DOI

      10.1371/journal.pone.0080448

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Community-wide evaluation of methods forpredicting the effect of mutations on protein–protein interactions.2013

    • Author(s)
      Rocco Moretti, …, Eiji Kanamori, Yuko Tsuchiya, Haruki Nakamura, et al.
    • Journal Title

      Proteins

      Volume: 81 Issue: 11 Pages: 1980-1987

    • DOI

      10.1002/prot.24356

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies2013

    • Author(s)
      Katayama T, Wilkinson MD, Micklem G, Kawashima S, Yamaguchi A, Nakao M,Yamamoto Y, Okamoto S, Oouchida K, Chun HW, Aerts J, Afzal H, Antezana E, Arakawa K, Aranda B, Belleau F, Bolleman J, Bonnal RJ, Chapman B, Cock PJ, Eriksson T, Gordon PM, Goto N, Hayashi K, Horn H, Ishiwata R, Kaminuma E, Kasprzyk A, Kawaji H, Kido N, Kim YJ,Kinjo AR, Konishi F, Kwon KH, Labarga A, Lamprecht AL, Lin Y, Lindenbaum P, McCarthy L, Morita H, Murakami K, Nagao K, Nishida K, Nishimura K, Nishizawa T, Ogishima S, Ono K, Oshita K, Park KJ, Prins P, Saito TL, Samwald M, SatagopamVP, Shigemoto Y, Smith R, Splendiani A, Sugawara H, Taylor J, Vos RA, Withers D, Yamasaki C, Zmasek CM, Kawamoto S, Okubo K, Asai K, Takagi T.
    • Journal Title

      J Biomed Semantics

      Volume: 4(1) Issue: 1 Pages: 6-6

    • DOI

      10.1186/2041-1480-4-6

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [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)
      Higo, J., Umezawa, K., Nakamura, H.
    • Journal Title

      Journal of Chemical Physics

      Volume: 138

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Composite structural motifs of binding sites for delineating biological functions of proteins2012

    • Author(s)
      Kinjo AR, Nakamura H
    • Journal Title

      PLoS One

      Volume: 7 Issue: 2 Pages: e31437-e31437

    • DOI

      10.1371/journal.pone.0031437

    • Related Report
      2013 Final Research Report 2011 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
      2013 Final Research Report 2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Counterbalance of ligand- and self-coupled motions characterizes multispecificity of ubiquitin2012

    • Author(s)
      Dasgupta B, Nakamura H, Kinjo AR
    • Journal Title

      Protein Science

      Volume: 22 Issue: 2 Pages: 168-178

    • DOI

      10.1002/pro.2195

    • Related Report
      2013 Final Research Report 2011 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] Enhanced and effective conformational sampling of protein molecular systems for their free energy landscapes2012

    • Author(s)
      Higo, J., Ikebe, J., Kamiya, N., Nakamura, H
    • Journal Title

      Biophysical Rev

      Volume: 4 Issue: 1 Pages: 27-44

    • DOI

      10.1007/s12551-011-0063-6

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Conformational Ensembles of an Intrinsically Disordered Protein pKID with and without a KIX Domain in Explicit Solvent Investigated by All-Atom Multicanonical Molecular Dynamics2012

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

      Biomolecules

      Volume: 2 Issue: 1 Pages: 104-121

    • DOI

      10.3390/biom2010104

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] GIRAF: a method for fast search and flexible alignment of ligand binding interfaces in proteins at atomic resolution2012

    • Author(s)
      Kinjo AR, Nakamura H
    • Journal Title

      BIOPHYSICS

      Volume: 8 Issue: 0 Pages: 79-94

    • DOI

      10.2142/biophysics.8.79

    • NAID

      130002061589

    • ISSN
      1349-2942
    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Computer-aided antibody design.2012

    • Author(s)
      Kuroda, D., Shirai, H., Jacobson, M. P., Nakamura, H.
    • Journal Title

      Protein Engineering, Design and Selection

      Volume: 25 Issue: 10 Pages: 507-521

    • DOI

      10.1093/protein/gzs024

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Distinct roles of overlapping and non-overlapping regions of hub protein interfaces in recognition of multiple partners2011

    • Author(s)
      Dasgupta B, Nakamura H, Kinjo AR
    • Journal Title

      Journal of Molecular Biology

      Volume: 411 Issue: 3 Pages: 713-727

    • DOI

      10.1016/j.jmb.2011.06.027

    • Related Report
      2013 Final Research Report 2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Community-Wide Assessment of Protein-Interface Modeling Suggests Improvements to Design Methodology2011

    • Author(s)
      Fleishman SJ, 他(研究代表者含む,全96人)
    • Journal Title

      Journal of Molecular Biology

      Volume: 414 Issue: 2 Pages: 289-302

    • DOI

      10.1016/j.jmb.2011.09.031

    • Related Report
      2013 Final Research Report 2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Free-energy Landscape for Coupled Folding and Binding of an Intrinsically Disordered Protein in Explicit Solvent from Detailed All-atom Computations2011

    • Author(s)
      Higo J, Nishimura Y, Nakamura H
    • Journal Title

      J Am Chem Soc

      Volume: 133 Issue: 27 Pages: 10448-10458

    • DOI

      10.1021/ja110338e

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Presentation] New Approach to Electrostatic Properties of Proteins and Protein-Protein Interactions2014

    • Author(s)
      Nakamura H
    • Organizer
      The 4th Asia Pacific Protein Association (APPA) Conference
    • Place of Presentation
      ICC Jeju, Korea
    • Year and Date
      2014-05-18
    • Related Report
      2013 Final Research Report
    • Invited
  • [Presentation] New Approaches to Dynamic Properties of Proteins and their Applications to Drug Discover of GPCR2013

    • Author(s)
      Nakamura H
    • Organizer
      CADD'13
    • Place of Presentation
      Institut Teknologi Bandung, Bandung, Indonesia
    • Year and Date
      2013-12-12
    • Related Report
      2013 Final Research Report
    • Invited
  • [Presentation] 蛋白質の結合部位の構造パターンと 生物学的機能を結ぶ2013

    • Author(s)
      金城玲
    • Organizer
      第6回定量生物学の会
    • Place of Presentation
      大阪大学銀杏会館
    • Year and Date
      2013-11-24
    • Related Report
      2013 Final Research Report
    • Invited
  • [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 Final Research Report
    • Invited
  • [Presentation] Composite structural motifs of binding sites for annotating functional differences2013

    • Author(s)
      Kinjo AR
    • Organizer
      International Conference on Structural Genomics 2013
    • Place of Presentation
      京王プラザホテル札幌
    • Year and Date
      2013-07-29
    • Related Report
      2013 Final Research Report
    • Invited
  • [Presentation] Composite structural motifs of binding sites for delineating biological functions of proteins2013

    • Author(s)
      金城玲
    • Organizer
      第54回植物生理学会年会
    • Place of Presentation
      岡山大学
    • Year and Date
      2013-03-21
    • Related Report
      2013 Final Research Report
    • Invited
  • [Presentation] 生命科学における情報科学・計算科学2013

    • 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
    • Year and Date
      2013-02-22
    • Related Report
      2013 Final Research Report 2012 Annual Research Report
    • Invited
  • [Presentation] Drug Development for a GPCR with in-silico screening2013

    • Author(s)
      Nakamura H
    • Organizer
      Nagoya symposium : Frontiers in Structural Physiology
    • Place of Presentation
      名古屋大学豊田講堂
    • Year and Date
      2013-01-24
    • Related Report
      2013 Final 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 systems2013

    • Author(s)
      Nakamura H
    • 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
    • Year and Date
      2013-01-14
    • Related Report
      2013 Final Research Report
    • Invited
  • [Presentation] Prediction of protein-protein complex structures2013

    • Author(s)
      Nakamura H
    • Organizer
      International Conference on Biomolecular Forms and Functions
    • Place of Presentation
      Indian Institute of Science Bangalore, India
    • Year and Date
      2013-01-10
    • Related Report
      2013 Final 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)
    • 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, Boston, USA
    • Related Report
      2013 Annual Research Report
  • [Presentation] Free-energy Landscape of Coupled Folding and Binding of IDP-partner Systems in an Explicit Solvent Investigated by All-atom Multicanonical Molecular Dynamics2013

    • Author(s)
      Junichi Higo, Koji Umezawa, Haruki Nakamura
    • Organizer
      Protein Society the 27th Annual Symposium
    • Place of Presentation
      Boston Marriott, Boston, USA
    • Related Report
      2013 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
    • Related Report
      2013 Annual Research Report
  • [Presentation] 蛋白質の自由エネルギー地形2012

    • Author(s)
      中村春木
    • Organizer
      スーパーコンピュータ・ワークショップ2012
    • Place of Presentation
      自然科学研究機構・岡崎コンファレンスセンター
    • Year and Date
      2012-01-25
    • Related Report
      2013 Final Research Report 2011 Annual Research Report
    • Invited
  • [Presentation] Zero-dipole summation法を用いた、DNAおよびタンパク質-DNA複合体の分子動力学シミュレーション2012

    • Author(s)
      中村 春木
    • Organizer
      第12回日本蛋白質科学会年会
    • Place of Presentation
      名古屋国際会議場
    • Related Report
      2011 Annual Research Report
  • [Presentation] 蛋白質-蛋白質ドッキングのためのスコア関数の開発:抗原抗体の場合2012

    • Author(s)
      中村 春木
    • Organizer
      第12回日本蛋白質科学会年会
    • Place of Presentation
      名古屋国際会議場
    • Related Report
      2011 Annual Research Report
  • [Presentation] 蛋白質相互作用部位構造の高速検索と柔軟なアラインメント法2012

    • Author(s)
      金城 玲
    • Organizer
      第12回日本蛋白質科学会年会
    • Place of Presentation
      名古屋国際会議場
    • Related Report
      2011 Annual Research Report
  • [Presentation] 抗原抗体相互作用における親和性創出機構の精密解析2012

    • Author(s)
      中村 春木
    • Organizer
      第12回日本蛋白質科学会年会
    • Place of Presentation
      名古屋国際会議場
    • Related Report
      2011 Annual Research Report
  • [Presentation] GPUを利用したZero-dipole summation法をによる静電相互作用の高速計算2012

    • Author(s)
      中村 春木
    • Organizer
      第12回日本蛋白質科学会年会
    • Place of Presentation
      名古屋国際会議場
    • Related Report
      2011 Annual Research Report
  • [Presentation] Prediction of Protein-Protein Complex Structures Using a Docking Server, surFit2012

    • Author(s)
      Nakamura, H.
    • Organizer
      The 26th Annual Symposium of the Protein Society
    • Place of Presentation
      Manchester Grand Hyatt, San Diego, California, USA
    • Related Report
      2011 Annual Research Report
  • [Presentation] 3D complex structure assignment for evolutionary conserved protein-protein interactions2012

    • Author(s)
      金城 玲
    • Organizer
      第50回日本生物物理学会年会
    • Place of Presentation
      名古屋大学東山キャンパス
    • Related Report
      2011 Annual Research Report
  • [Presentation] Molecular dynamics simulations of dynein motor domain in explicit water2012

    • Author(s)
      神谷 成敏
    • Organizer
      第50回日本生物物理学会年会
    • Place of Presentation
      名古屋大学東山キャンパス
    • Related Report
      2011 Annual Research Report
  • [Presentation] Molecular Dynamics Simulations of Ets1-DNA complexes using Zero-Dipole Summation Method2012

    • Author(s)
      中村 春木
    • Organizer
      第50回日本生物物理学会年会
    • Place of Presentation
      名古屋大学東山キャンパス
    • Related Report
      2011 Annual Research Report
  • [Presentation] A simple non-Ewald scheme: the zero-dipole summation method and its application to molecular systems2012

    • Author(s)
      Nakamura, H.
    • Organizer
      Conference on Computational Physics (CCP2012)
    • Place of Presentation
      Nichii Gakkan, Kobe
    • Related Report
      2011 Annual Research Report
  • [Presentation] Prediction of protein-protein complex structures2012

    • Author(s)
      Nakamura, H.
    • Organizer
      International Conference on Biomolecular Forms and Functions
    • Place of Presentation
      Indian Institute of Science, Bangalore, India
    • Related Report
      2011 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 systems2012

    • Author(s)
      Nakamura, H.
    • Organizer
      National Symposium on Frontiers of Biophysics, Biotechnology & Bioinformatics and 37'th Annual Meeting of Indian Biophysical Society
    • Place of Presentation
      University of Mumbai, Mumbai, India
    • Related Report
      2011 Annual Research Report
    • Invited
  • [Presentation] Computational Prediction and Analysis of Protein-Protein Interactions: Qualitative and Quantitative Approaches2012

    • Author(s)
      Nakamura, H.
    • Organizer
      Special Seminar at Academia Sinica
    • Place of Presentation
      Academia Sinica, Shanghai, China
    • Related Report
      2011 Annual Research Report
    • Invited
  • [Presentation] Drug Development for a GPCR with in-silico screening2012

    • Author(s)
      Nakamura, H.
    • Organizer
      Nagoya Symposium
    • Place of Presentation
      名古屋大学 豊田講堂
    • Related Report
      2011 Annual Research Report
    • Invited
  • [Presentation] Intrinsically Disordered Proteins and Development of Corresponding Drugs2011

    • Author(s)
      Nakamura H
    • Organizer
      CADD2011 (Plenary Lecture)
    • Place of Presentation
      Penang, Malaysia
    • Year and Date
      2011-12-05
    • Related Report
      2013 Final Research Report 2011 Annual Research Report
    • Invited
  • [Presentation] Structural properties of hub proteins in interaction networks and its implications on interaction promiscuity2011

    • Author(s)
      中村 春木
    • Organizer
      第11回日本蛋白質科学会年会
    • Place of Presentation
      大阪千里
    • Related Report
      2011 Annual Research Report
  • [Presentation] 抗原・抗体間のフレキシブルドッキング・マルチカノニカル分子動力学シミュレーション2011

    • Author(s)
      神谷 成敏
    • Organizer
      第11回日本蛋白質科学会年会
    • Place of Presentation
      大阪千里
    • Related Report
      2011 Annual Research Report
  • [Presentation] 天然変死蛋白質NRSFとそのパートナー蛋白質mSin3の結合/折れ畳みの詳細な自由エネルギー地形2011

    • Author(s)
      肥後 順一
    • Organizer
      第11回日本蛋白質科学会年会
    • Place of Presentation
      大阪千里
    • Related Report
      2011 Annual Research Report
  • [Presentation] 蛋白質の生物学的機能解析のための相互作用界面の複合構造モチーフ2011

    • Author(s)
      金城 玲
    • Organizer
      第49回日本生物物理学会
    • Place of Presentation
      兵庫県立大学
    • Related Report
      2011 Annual Research Report
  • [Presentation] ハブ蛋白質のリガンド依存構造変化:ユビキチンの場合2011

    • Author(s)
      金城 玲
    • Organizer
      第49回日本生物物理学会
    • Place of Presentation
      兵庫県立大学
    • Related Report
      2011 Annual Research Report
  • [Presentation] 全原子シミュレーションによる天然変性蛋白質の自由エネルギー地形2011

    • Author(s)
      肥後 順一
    • Organizer
      第49回日本生物物理学会
    • Place of Presentation
      兵庫県立大学
    • Related Report
      2011 Annual Research Report
  • [Presentation] Free Energy Landscape: the road map for protein conformational changes2011

    • Author(s)
      肥後 順一
    • Organizer
      第34回日本分子生物学会年会シンポジウム
    • Place of Presentation
      パシフィコ横浜
    • Related Report
      2011 Annual Research Report
    • Invited
  • [Presentation] Prediction of Protein-Protein Interactions: Structural Approaches

    • Author(s)
      Haruki Nakamura
    • Organizer
      The 2nd HD Physiology International Symposium
    • Place of Presentation
      丸の内MY PLAZAホール(東京)
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] Composite structural motifs of binding sites for annotating functional differences

    • Author(s)
      Akira R. Kinjo
    • Organizer
      International Conference on Structural Genomics 2013
    • Place of Presentation
      京王プラザホテル札幌(札幌市)
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] ゲノム情報(1D)から蛋白質の動的構造情報(4D)へ

    • 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)
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] 蛋白質の結合部位の構造パターンと生物学的機能を結ぶ

    • Author(s)
      金城 玲
    • Organizer
      第6回定量生物学の会
    • Place of Presentation
      大阪大学銀杏会館(吹田市)
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] New Approaches to Dynamic Properties of Proteins and their Applications to Drug Discover of GPCR.

    • Author(s)
      Haruki Nakamura
    • Organizer
      CADD’13
    • Place of Presentation
      Bandung, Indonesia
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] Computational Protein Science: Structural Bioinformatics and Molecular Simulations

    • Author(s)
      Haruki Nakamura
    • Organizer
      CDAST symposium
    • Place of Presentation
      Jember University, Indonesia
    • Related Report
      2013 Annual Research Report
    • Invited
  • [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 Fukuda1, 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] SGDDによるGPCRに対する非ペプチド性アゴニストの開発

    • Author(s)
      中村春木
    • Organizer
      第12回 プロテインモール関西情報交流セミナー
    • Place of Presentation
      千里ライフサイエンスセンター(大阪)
    • Related Report
      2012 Annual Research Report
    • Invited
  • [Presentation] Composite structural motifs of binding sites for delineating biological functions of protein

    • Author(s)
      金城 玲
    • Organizer
      第54回植物生理学会年会
    • Place of Presentation
      岡山大学
    • Related Report
      2012 Annual Research Report
    • Invited
  • [Book] "Prediction of Protein-Protein Complex Structures" in 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 DM, Shirota M, Kinoshita K, Tsuchiya Y, Higo J, Nakamura H
    • Publisher
      World Scientific Publishing
    • Related Report
      2013 Final Research Report
  • [Book] Biomolecular Forms and Functions2013

    • Author(s)
      Kanamori, E.
    • Total Pages
      502
    • Publisher
      World Scientific Publishing
    • Related Report
      2011 Annual Research Report
  • [Remarks]

    • URL

      http://www.protein.osaka-u.ac.jp/rcsfp/pi/index_pi.html

    • Related Report
      2013 Final Research Report

URL: 

Published: 2011-04-06   Modified: 2019-07-29  

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