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Structural Interactome Studies from Computational and Bioinformatics Approaches

Research Project

Project/Area Number 20370061
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  Osaka University, 蛋白質研究所, 教授 (80134485)

Co-Investigator(Kenkyū-buntansha) KINOSHITA Kengjo  東北大学, 大学院・情報科学研究科, 教授 (60332293)
Co-Investigator(Renkei-kenkyūsha) HIGO Junichi  大阪大学, 蛋白質研究所, 特任研究員(客員教授) (80265719)
KAMIYA Narutoshi  大阪大学, 蛋白質研究所, 特任研究員(客員准教授) (80420462)
Project Period (FY) 2008 – 2010
Project Status Completed (Fiscal Year 2010)
Budget Amount *help
¥20,150,000 (Direct Cost: ¥15,500,000、Indirect Cost: ¥4,650,000)
Fiscal Year 2010: ¥6,500,000 (Direct Cost: ¥5,000,000、Indirect Cost: ¥1,500,000)
Fiscal Year 2009: ¥6,500,000 (Direct Cost: ¥5,000,000、Indirect Cost: ¥1,500,000)
Fiscal Year 2008: ¥7,150,000 (Direct Cost: ¥5,500,000、Indirect Cost: ¥1,650,000)
Keywords生物物理 / 蛋白質の構造・機能予測 / 生体分子 / プロテオーム / 分子動力学 / バイオインフォマティクス / データベース / 蛋白質間相互作用
Research Abstract

For structural interactome study, which investigates the protein-protein interaction network based on their tertiary structures, we have constructed several different kinds of databases and made informatics analyses by identifying and predicting the interfaces, so that complex structural models have been predicted. In addition, for the intrinsically denatured proteins, we have successfully reproduced and analyzed their coupled folding and binding procedures as the stable states in the free energy landscapes from computational studies.

Report

(4 results)
  • 2010 Annual Research Report   Final Research Report ( PDF )
  • 2009 Annual Research Report
  • 2008 Annual Research Report
  • Research Products

    (144 results)

All 2011 2010 2009 2008 Other

All Journal Article (51 results) (of which Peer Reviewed: 51 results) Presentation (80 results) Book (5 results) Remarks (8 results)

  • [Journal Article] Theory for trivial trajectory parallelization of multicanonical molecular dynamics and application to a polypeptide in water.2011

    • Author(s)
      J.Ikebe, K.Umezawa, N.Kamiya, T.Sugihara, Y.Yonezawa, Y.Takano, H.Nakamura, J.Higo
    • Journal Title

      J.Comput.Chem. 32

      Pages: 1286-1297

    • Related Report
      2010 Final Research Report
    • Peer Reviewed
  • [Journal Article] Absolute quality evaluation of protein model structures using statistical potentials with respect to the native and reference states.2011

    • Author(s)
      M.Shirota, T.Ishida, K.Kinoshita
    • Journal Title

      PROTEINS 79

      Pages: 1550-1563

    • Related Report
      2010 Final Research Report
    • Peer Reviewed
  • [Journal Article] HitPredict : a database of quality assessed protein-protein interactions in 9 species.2011

    • Author(s)
      A.Patil, K.Nakai, H.Nakamura
    • Journal Title

      Nucl.Acids Res 39

    • Related Report
      2010 Final Research Report
    • Peer Reviewed
  • [Journal Article] COXPRESdb : a database to compare gene coexpression in seven model animals.2011

    • Author(s)
      T.Obayashi, K.Kinoshita
    • Journal Title

      Nucl.Acids Res. 39

    • Related Report
      2010 Final Research Report
    • Peer Reviewed
  • [Journal Article] Ab initio simulation of a 57-residue protein in explicit solvent reproduces the native conformation in the lowest free-energy cluster.2011

    • Author(s)
      J.Ikebe, D.M.Standley, H.Nakamura, J.Higo
    • Journal Title

      Protein Science 20

      Pages: 187-196

    • Related Report
      2010 Final Research Report
    • Peer Reviewed
  • [Journal Article] Ab initio simulation of a 57-residue protein in explicit solvent reproduces the native conformation in the lowest free-energy cluster2011

    • Author(s)
      Jinzen Ikebe
    • Journal Title

      Protein Science

      Volume: 20 Pages: 187-196

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] HitPredict : a database of quality assessed protein-protein interactions in 9 species2011

    • Author(s)
      Ashwini Patil
    • Journal Title

      Nucl.Acids Res.

      Volume: 39

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Multicanonical Molecular Dynamics Simulations Combined with MetaDynamics for the Free Energy Landscape of a Biomolecular System with High Energy Barriers2011

    • Author(s)
      Yasushige Yonezawa
    • Journal Title

      Chem.Phys.Lett.

      Volume: 501 Pages: 598-602

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Simple and effective application of the Wang-Landau method for multicanonical molecular dynamics simulation2011

    • Author(s)
      Hiromitsu Shimoyama
    • Journal Title

      J.Chem.Phys.

      Volume: 134

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Degree of Pyramidality Governs the Height and Peak position of the Free-Energy-Barrier for the cis-trans Isomerization of N-Methylacetamide2011

    • Author(s)
      Yasushige Yonezawa
    • Journal Title

      Chem.Phys.Lett.

      Volume: 503 Pages: 139-144

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Intrinsic Electronic Structures of the Novel [4Fe-4S] Cluster Found in Dark-operative Protochlorophyllide Oxidoreductase (DPOR)2011

    • Author(s)
      Yu Takano
    • Journal Title

      Chem.Phys.Lett.

      Volume: 503 Pages: 296-300

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] COXPRESdb : a database to compare gene coexpression in seven model animals2011

    • Author(s)
      Takeshi Obayashi
    • Journal Title

      Nuc.Acids Res.

      Volume: 39

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Domain distribution and intrinsic disorder in hubs in the human protein-protein interaction network.2010

    • Author(s)
      A.Patil, K.Kinoshita, H.Nakamura
    • Journal Title

      Protein Science 19

      Pages: 1461-1468

    • Related Report
      2010 Final Research Report
    • Peer Reviewed
  • [Journal Article] Geometric similarities of protein-protein interfaces at atomic resolution are only observed within homologous families : An exhaustive structural classification study.2010

    • Author(s)
      A.R.Kinjo, H.Nakamura
    • Journal Title

      J.Mol.Biol. 399

      Pages: 526-540

    • Related Report
      2010 Final Research Report
    • Peer Reviewed
  • [Journal Article] Structural properties of hubs in protein-protein interaction networks.2010

    • Author(s)
      A.Patil, K.Kinoshita, H.Nakamura
    • Journal Title

      Int.J.Mol.Sci. 11

      Pages: 1930-1943

    • Related Report
      2010 Final Research Report
    • Peer Reviewed
  • [Journal Article] SeSAW : balancing sequence and structural information in protein function mapping2010

    • Author(s)
      Daron M.Standley
    • Journal Title

      Bioinformatics

      Volume: 26 Pages: 1258-1259

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Evaluation of the conformational equilibrium of reduced hen egg lysozyme by antibodies to the native form2010

    • Author(s)
      Masayuki Oda
    • Journal Title

      Arch.Biochem.Biophys.

      Volume: 494 Pages: 145-150

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Structural properties of hubs in protein-protein interaction networks2010

    • Author(s)
      Ashwini Patil
    • Journal Title

      Int.J.Mol.Sci.

      Volume: 11 Pages: 1930-1943

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Solvent flow patterns fluctuating largely around a protein and correlation with solvent density fluctuations : a molecular dynamics study2010

    • Author(s)
      Koji Umezawa
    • Journal Title

      J.Chem.Phys.

      Volume: 132

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Geometric similarities of protein-protein interfaces at atomic resolution are only observed within homologous families : An exhaustive structural classification study2010

    • Author(s)
      Akira R.Kinjo
    • Journal Title

      J.Mol.Biol.

      Volume: 399 Pages: 526-540

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] PiRaNhA : a server for the computational prediction of RNA-binding residues in protein2010

    • Author(s)
      Yoichi Murakami
    • Journal Title

      Nucl.Acids Res.

      Volume: 38

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Domain distribution and intrinsic disorder in hubs in the human protein-protein interaction network2010

    • Author(s)
      Ashwini Patil
    • Journal Title

      Protein Science

      Volume: 19 Pages: 1461-1468

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Enhanced free-energy calculation using multi-scale simulation2010

    • Author(s)
      Hiromitsu Shimoyama
    • Journal Title

      J.Chem.Phys.

      Volume: 133

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Creation of a Type 1 Blue Copper Site within a de Novo Coiled-coil Protein Scaffold2010

    • Author(s)
      Daigo Shiga
    • Journal Title

      J.Am.Chem.Soc.

      Volume: 132 Pages: 18191-18198

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Absolute quality evaluation of protein model structures using statistical potentials with respet to the native and reference states2010

    • Author(s)
      Matsuyuki Shirota
    • Journal Title

      Proteins

      Volume: (In press)

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Electronic structures of heme a of cytochrome c oxidase in the redoc states -Charge density migration to the nronionate groups of heme a-2010

    • Author(s)
      Yu Takano
    • Journal Title

      J.Comput.Chem. 31

      Pages: 954-962

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] 蛋白質計算科学のさらなる発展を目指して:次世代スーパリコンピュータによるヘテロでダイナミックな蛋白質の電子構造解析2010

    • Author(s)
      米澤康滋
    • Journal Title

      生産と技術 62

      Pages: 89-91

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Classification of heterodimer interfaces using docking models and construction of scoring functions for the complex structure prediction.2009

    • Author(s)
      Y.Tsuchiya, E.Kanamori, H.Nakamura, K.Kinoshita
    • Journal Title

      Adv.Appl.Bioinfo.Chem. 2

      Pages: 79-10

    • Related Report
      2010 Final Research Report
    • Peer Reviewed
  • [Journal Article] ATTED-II provides coexpressed gene networks for Arabidopsis.2009

    • Author(s)
      T.Obayashi, S.Hayashi, M.Saeki, H.Ohta, K.Kinoshita
    • Journal Title

      Nucl.Acids Res. 37

    • Related Report
      2010 Final Research Report
    • Peer Reviewed
  • [Journal Article] Intra- and Intermolecular Interaction Inducing Pyramidalization on both sides of a Proline Di-peptide during Isomerization : an ab Initio QM/MM Molecular Dynamics Simulation Study in explicit water2009

    • Author(s)
      Yasushige Yonezawa
    • Journal Title

      J.Ame.Chem.Soc. 131

      Pages: 4535-4540

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Conformational requirement on peptides to exert laminin's activities and search for protein segments with the laminin's activities2009

    • Author(s)
      Koji Umezawa
    • Journal Title

      Biopolymers : Peptide Science 92

      Pages: 124-131

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Classification of hetero-dimer interfaces using docking models and construction of scoring functions for the complex structure prediction2009

    • Author(s)
      Yuko Tsuchiya
    • Journal Title

      Adv.Appl.Bioinfo.Chem. 2

      Pages: 79-100

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Numerical examination of the extended phase-space volume-preserving integrator by the Nose-Hoover molecular dynamics equations2009

    • Author(s)
      Severine Queyroy
    • Journal Title

      J.Comput.Chem. 30

      Pages: 1799-1815

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] The CCCH-type zinc finger protein, Zc3hl2a, is a ribonuclease essential for controlling immune responses by regulating mRNA decay2009

    • Author(s)
      Kazufumi Matsushita
    • Journal Title

      Nature 458

      Pages: 1185-1190

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Hybrid-DFT study on electronic structures of the active site of sweet poteto purple acid phosphatase -The origin of stronger antiferromagnetic coupling than other purple acid phosphatase-2009

    • Author(s)
      Kenichi Koizumi
    • Journal Title

      J.Phys.Chem.A 113

      Pages: 5099-5104

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Verifying trivial parallelization of multicanonical molecular dynamics for conformational sampling of a polypeptide in explicit water2009

    • Author(s)
      Junichi Higo
    • Journal Title

      Chem.Phys.Lett. 473

      Pages: 326-329

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Protein function annotation from sequence, PiRaNhA : prediction of specific RNA-binding residues2009

    • Author(s)
      Ruth V.Spriggs
    • Journal Title

      Bioinformatics 25

      Pages: 1492-1497

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Membrane attachment facilitates ligand access to active site in Monoamine oxidase A2009

    • Author(s)
      Rossen P.Apostolov
    • Journal Title

      Biochemistry 48

      Pages: 5864-5873

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Parallelization of Markov Chain Generation and its Application to the Multicacnonical Method2009

    • Author(s)
      Takanori Sugihara
    • Journal Title

      J.Phys.Soc.Jpn. 78

      Pages: 74003-74003

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Theoretical studies of the magnetic couplings and the chemical indices of the biomimetic models of oxvhemocvanin and oxvtvrosinase2009

    • Author(s)
      Yu Takano
    • Journal Title

      Inorganic Chim.Acta 362

      Pages: 4578-4584

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Density functional study of roles of porphyrin ring in electronic structures of heme2009

    • Author(s)
      Yu Takano
    • Journal Title

      Int.J.Quantum Chem. 109

      Pages: 3583-3591

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Design of the distorted coordination structure of Cu^<2+> in a de novo designed protein2009

    • Author(s)
      Daigo Shiga
    • Journal Title

      Biopolvmers 91

      Pages: 907-916

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Development of a new meta-score for protein structure prediction from seven all-atom distance dependent potentials using support vector regression2009

    • Author(s)
      Matsuyuki Shirota
    • Journal Title

      Genome Informatics 23

      Pages: 149-158

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Resonating coupled-cluster CI approach to Ion-radical systems : Comparison with the unrestricted coupled-cluster approach2009

    • Author(s)
      Shusuke Yamanaka
    • Journal Title

      Int.J.Quantum Chem. 109

      Pages: 3811-3818

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Systematic classification of CDR-L3 in antibodies : Implications of thelight chain sub-types and the V_L-V_H interface.2009

    • Author(s)
      Daisuke Kuroda
    • Journal Title

      PROTEINS 75

      Pages: 139-146

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] ATTED-II provides coexpressed gene networks for Arabidopsis2009

    • Author(s)
      Takeshi Obayashi
    • Journal Title

      Nucleic Ac ids Research 37

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Discrimination between biological interfaces and crystal-packing contacts.2008

    • Author(s)
      Y.Tsuchiya, H.Nakamura, K.Kinoshita
    • Journal Title

      Comput.Biol.Chem. 1

      Pages: 99-113

    • Related Report
      2010 Final Research Report
    • Peer Reviewed
  • [Journal Article] Structural classification of CDR-H3 revisited : a lesson in antibody modeling.2008

    • Author(s)
      Daisuke Kuroda
    • Journal Title

      PROTEINS 73

      Pages: 608-620

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Discrimination between biological interfaces and crystal-packing contacts.2008

    • Author(s)
      Yuko Tsuchiya
    • Journal Title

      Computational Biology and Chemistry 1

      Pages: 99-113

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Consistent molecular dynamics scheme applying the Wolf summation for calculating electrostatic interaction of particles.2008

    • Author(s)
      Ikuo Fukuda
    • Journal Title

      Journal of Physical Society of Japan 77

      Pages: 114301-114301

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] In sillico prediction of the chemical block of human ether-a-gogo-relatedgene (hERG)K十current.2008

    • Author(s)
      Atsushi Inanobe
    • Journal Title

      Journal of Physiological Science 58

      Pages: 459-470

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Presentation] PDBj : Protein structural database and query system for protein functions2010

    • Author(s)
      Haruki Nakamura
    • Organizer
      International CD and Bioinformatics Conference
    • Place of Presentation
      Warwick University, UK(招待講演)
    • Year and Date
      2010-12-03
    • Related Report
      2010 Annual Research Report
  • [Presentation] ProMode-Elastic : database of elastic-network-model based normal mode analysis2010

    • Author(s)
      Haruki Nakamura
    • Organizer
      International Conference on Bioinformatics (InCoB2010)
    • Place of Presentation
      早稲田大学、東京
    • Year and Date
      2010-09-27
    • Related Report
      2010 Annual Research Report
  • [Presentation] High-throughput and Low-resolution structure comparison of 3D electron microscopy data2010

    • Author(s)
      中村春木
    • Organizer
      第48回生物物理学会年会
    • Place of Presentation
      東北大学、仙台
    • Year and Date
      2010-09-22
    • Related Report
      2010 Annual Research Report
  • [Presentation] Structural modeling for protein complexes using small angle x-ray scattering2010

    • Author(s)
      中村春木
    • Organizer
      第48回生物物理学会年会
    • Place of Presentation
      東北大学、仙台
    • Year and Date
      2010-09-22
    • Related Report
      2010 Annual Research Report
  • [Presentation] Estimation of native-like state of protein structure using statistical potentials for protein structure prediction2010

    • Author(s)
      木下賢吾
    • Organizer
      第48回生物物理学会年会
    • Place of Presentation
      東北大学、仙台
    • Year and Date
      2010-09-22
    • Related Report
      2010 Annual Research Report
  • [Presentation] Study on 4'-Phosphopantetheinyl Transfer Reactions to Acyl Carrier Protein : the Preliminary Processes of Human Fatty Acid Synthesis2010

    • Author(s)
      中村春木
    • Organizer
      第48回生物物理学会年会
    • Place of Presentation
      東北大学、仙台
    • Year and Date
      2010-09-21
    • Related Report
      2010 Annual Research Report
  • [Presentation] Simple and easy application of Wang-Landau method to molecular dynamics simulations2010

    • Author(s)
      中村春木
    • Organizer
      第48回生物物理学会年会
    • Place of Presentation
      東北大学、仙台
    • Year and Date
      2010-09-21
    • Related Report
      2010 Annual Research Report
  • [Presentation] Conformational transition in the CDRH3 region of the anti-dansyl monoclonal antibody by molecular dynamics simulations2010

    • Author(s)
      中村春木
    • Organizer
      第48回生物物理学会年会
    • Place of Presentation
      東北大学、仙台
    • Year and Date
      2010-09-20
    • Related Report
      2010 Annual Research Report
  • [Presentation] Electronic structures of the novel [4F-4S] cluster in dark-operative protochlorophyllide oxidoreductase2010

    • Author(s)
      中村春木
    • Organizer
      第48回生物物理学会年会
    • Place of Presentation
      東北大学、仙台
    • Year and Date
      2010-09-20
    • Related Report
      2010 Annual Research Report
  • [Presentation] Conservation of protein-ligand interactions : a data-mining of the PDB by using Gaussian mixture model2010

    • Author(s)
      木下賢吾
    • Organizer
      第48回生物物理学会年会
    • Place of Presentation
      東北大学、仙台
    • Year and Date
      2010-09-20
    • Related Report
      2010 Annual Research Report
  • [Presentation] 粗視化モデルによる脂肪酸合成酵素の構造変化シミュレーション2010

    • Author(s)
      中村春木
    • Organizer
      第10回日本蛋白質科学会年会
    • Place of Presentation
      札幌コンベンションセンター・札幌
    • Year and Date
      2010-06-18
    • Related Report
      2010 Annual Research Report
  • [Presentation] 補因子Fe_4S_4クラスターの酸化還元反応における電子構造の理論的研究2010

    • Author(s)
      中村春木
    • Organizer
      第10回日本蛋白質科学会年会
    • Place of Presentation
      札幌コンベンションセンター・札幌
    • Year and Date
      2010-06-18
    • Related Report
      2010 Annual Research Report
  • [Presentation] 低分解能3次元電子顕微鏡データのハイスループット構造比較2010

    • Author(s)
      中村春木
    • Organizer
      第10回日本蛋白質科学会年会
    • Place of Presentation
      札幌コンベンションセンター・札幌
    • Year and Date
      2010-06-18
    • Related Report
      2010 Annual Research Report
  • [Presentation] 自然免疫蛋白質の機能アノテーション2010

    • Author(s)
      中村春木
    • Organizer
      第10回日本蛋白質科学会年会
    • Place of Presentation
      札幌コンベンションセンター・札幌
    • Year and Date
      2010-06-18
    • Related Report
      2010 Annual Research Report
  • [Presentation] ヒトゲノム構造・機能アノテーションデータベースSAHGの構築2010

    • Author(s)
      木下賢吾
    • Organizer
      第10回日本蛋白質科学会年会
    • Place of Presentation
      札幌コンベンションセンター・札幌
    • Year and Date
      2010-06-18
    • Related Report
      2010 Annual Research Report
  • [Presentation] タンパク質-低分子化合物フラグメント間相互作用情報を利用した結合部位・結合構造の予測2010

    • Author(s)
      木下賢吾
    • Organizer
      第10回日本蛋白質科学会年会
    • Place of Presentation
      札幌コンベンションセンター・札幌
    • Year and Date
      2010-06-17
    • Related Report
      2010 Annual Research Report
  • [Presentation] 大量データと大規模計算機による蛋白質の構造・機能解析2010

    • Author(s)
      中村春木
    • Organizer
      日本蛋白質科学会
    • Place of Presentation
      札幌コンベンションセンター
    • Year and Date
      2010-06-16
    • Related Report
      2010 Final Research Report
  • [Presentation] 大量データと大規模計算機による蛋白質の構造・機能解析2010

    • Author(s)
      中村春木
    • Organizer
      第10回日本蛋白質科学会年会 シンポジウム 「蛋白質研究法先進計測・解析技術の新展開」
    • Place of Presentation
      札幌コンベンションセンター・札幌(招待講演)
    • Year and Date
      2010-06-16
    • Related Report
      2010 Annual Research Report
  • [Presentation] Domain distribution and intrinsic disorder in hubs in the human protein-protein interaction network2010

    • Author(s)
      中村春木
    • Organizer
      第10回日本蛋白質科学会年会
    • Place of Presentation
      札幌コンベンションセンター・札幌
    • Year and Date
      2010-06-16
    • Related Report
      2010 Annual Research Report
  • [Presentation] 単純並列化によるマルチカノニカル分子動力学法のサンプリング効率の向上2010

    • Author(s)
      肥後順一
    • Organizer
      第10回日本蛋白質科学会年会
    • Place of Presentation
      札幌コンベンションセンター・札幌
    • Year and Date
      2010-06-16
    • Related Report
      2010 Annual Research Report
  • [Presentation] QM/MM分子動力学シミュレーションによる脂肪酸合成に関わるアシルキャリアー蛋白質のホスフォパンテティン化酵素反応の研究2010

    • Author(s)
      中村春木
    • Organizer
      第10回日本蛋白質科学会年会
    • Place of Presentation
      札幌コンベンションセンター・札幌
    • Year and Date
      2010-06-16
    • Related Report
      2010 Annual Research Report
  • [Presentation] 光合成反応中心スペシャルペアの電子構造の蛋白質依存性2010

    • Author(s)
      中村春木
    • Organizer
      第10回日本蛋白質科学会年会
    • Place of Presentation
      札幌コンベンションセンター・札幌
    • Year and Date
      2010-06-16
    • Related Report
      2010 Annual Research Report
  • [Presentation] X線小角散乱を用いたタンパク質複合体の構造モデリングを目指して2010

    • Author(s)
      中村春木
    • Organizer
      第10回日本蛋白質科学会年会
    • Place of Presentation
      札幌コンベンションセンター・札幌
    • Year and Date
      2010-06-16
    • Related Report
      2010 Annual Research Report
  • [Presentation] 天然変性蛋白質pKIDのKIXドメインとの結合に共役したフォールディングのマルチカノニカル分子動力学計算による解析2010

    • Author(s)
      肥後順一
    • Organizer
      第10回日本蛋白質科学会年会
    • Place of Presentation
      札幌コンベンションセンター・札幌
    • Year and Date
      2010-06-16
    • Related Report
      2010 Annual Research Report
  • [Presentation] 蛋白質立体構造と複合体構造の評価関数の共通点と相違点2010

    • Author(s)
      木下賢吾
    • Organizer
      第10回日本蛋白質科学会年会
    • Place of Presentation
      札幌コンベンションセンター・札幌
    • Year and Date
      2010-06-16
    • Related Report
      2010 Annual Research Report
  • [Presentation] Bioinformatics and computational approaches to structural features in protein interactions for in-silico drug development.2010

    • Author(s)
      中村春木
    • Organizer
      The 1st international conference on frontiers of regenerative medicine and biomedical science.
    • Place of Presentation
      Jinan University, Guangzhoue(China)
    • Year and Date
      2010-05-14
    • Related Report
      2010 Final Research Report
  • [Presentation] Bioinformatics and Computational Approaches to Structural Features in Protein Interactions for in-silico Drug Development2010

    • Author(s)
      Haruki Nakamura
    • Organizer
      The 1st International Conference on Frontier4s of Regenerative Medicine and Biomedical Science
    • Place of Presentation
      Jinan University, Guangzhoue, China(招待講演)
    • Year and Date
      2010-05-14
    • Related Report
      2010 Annual Research Report
  • [Presentation] Structural Bioinformatics : Databases and Analyses2010

    • Author(s)
      Haruki Nakamura
    • Organizer
      The 9th China-Japan-Korea Bioinformatics Training Course and Bioinformatics Symposium
    • Place of Presentation
      Shanghai Institutes for Biological Sciences Chinese Academy of Sciences, Shanghai, China(招待講演)
    • Year and Date
      2010-04-21
    • Related Report
      2010 Annual Research Report
  • [Presentation] 計算科学によるタンパク質間相互作用の予測と解析2010

    • Author(s)
      中村春木
    • Organizer
      蛋白質立体構造解析NEDO特別講座、創薬シンポジウム
    • Place of Presentation
      東京大学薬学部,東京
    • Year and Date
      2010-03-09
    • Related Report
      2009 Annual Research Report
  • [Presentation] Application of distance dependent statistical pair potentials of protein folding to the evaluation of protein-protein interaction : Commonalities and differences between folding and docking.2010

    • Author(s)
      M. Shirota, K. Kasahara, Y. Tsuchiya, K. Kinoshita
    • Organizer
      MPI 2010
    • Place of Presentation
      Lawrence(USA)
    • Related Report
      2010 Final Research Report
  • [Presentation] Relationship between physics and information science in statistical potentials of protein structures.2010

    • Author(s)
      M. Shirota, T. Ishida, K. Kinoshita
    • Organizer
      AYRCOB 2010
    • Place of Presentation
      Tainan(Taiwan)
    • Related Report
      2010 Final Research Report
  • [Presentation] Prediction of function and protein-protein interaction by structural bioinformatics approach2009

    • Author(s)
      Haruki Nakamura
    • Organizer
      IISc Seminar
    • Place of Presentation
      Indian Institute of Science, Bangalore, India
    • Year and Date
      2009-12-17
    • Related Report
      2009 Annual Research Report
  • [Presentation] Bioinformatics and computational approaches to structural features in protein-protein interactions2009

    • Author(s)
      Haruki Nakamura
    • Organizer
      Bose Institute Seminar
    • Place of Presentation
      Bose Institute, Kolkata, India
    • Year and Date
      2009-12-16
    • Related Report
      2009 Annual Research Report
  • [Presentation] Electronic structures of biological molecules with their dynamic environments2009

    • Author(s)
      Haruki Nakamura
    • Organizer
      International Conference on Physics Biology Interface(ICPBI-2009)
    • Place of Presentation
      Saha Institute of Nulear Physics, Kolkata, India
    • Year and Date
      2009-12-15
    • Related Report
      2009 Annual Research Report
  • [Presentation] surFit : A Docking server of protein molecular surfaces2009

    • Author(s)
      Haruki Nakamura
    • Organizer
      4th CAPRI Evaluation Meeting
    • Place of Presentation
      Barcelona, Spain
    • Year and Date
      2009-12-09
    • Related Report
      2009 Annual Research Report
  • [Presentation] クロロフィル側鎖回転異性体の理論解析2009

    • Author(s)
      中村春木
    • Organizer
      第47回日本生物物理学会年会
    • Place of Presentation
      アスティとくしま、徳島
    • Year and Date
      2009-11-01
    • Related Report
      2009 Annual Research Report
  • [Presentation] Rhodobacter sphaeroides活性中心のAb initio QM/MMによる研究2009

    • Author(s)
      中村春木
    • Organizer
      第47回日本生物物理学会年会
    • Place of Presentation
      アスティとくしま、徳島
    • Year and Date
      2009-10-31
    • Related Report
      2009 Annual Research Report
  • [Presentation] 原子構造から電子構造の解析へ2009

    • Author(s)
      中村春木
    • Organizer
      第47回日本生物物理学会年会
    • Place of Presentation
      アスティとくしま、徳島
    • Year and Date
      2009-10-31
    • Related Report
      2009 Annual Research Report
  • [Presentation] スーパーコンピューティングによる蛋白質電子状態及び反応機構の解明に向けて2009

    • Author(s)
      中村春木
    • Organizer
      第47回日本生物物理学会年会
    • Place of Presentation
      アスティとくしま、徳島
    • Year and Date
      2009-10-31
    • Related Report
      2009 Annual Research Report
  • [Presentation] 粗視化モデルを用いた全原子シミュレーションの効率化2009

    • Author(s)
      中村春木
    • Organizer
      第47回日本生物物理学会年会
    • Place of Presentation
      アスティとくしま、徳島
    • Year and Date
      2009-10-31
    • Related Report
      2009 Annual Research Report
  • [Presentation] 天然変性蛋白質pKIDとKIXドメイン複合体形成における結合と折り畳みが共役した相互作用の計算科学による解析2009

    • Author(s)
      中村春木
    • Organizer
      第47回日本生物物理学会年会
    • Place of Presentation
      アスティとくしま、徳島
    • Year and Date
      2009-10-31
    • Related Report
      2009 Annual Research Report
  • [Presentation] 基準振動に基づく蛋白質-蛋白質相互作用の動的解析2009

    • Author(s)
      木下賢吾
    • Organizer
      第47回日本生物物理学会年会
    • Place of Presentation
      アスティとくしま、徳島
    • Year and Date
      2009-10-31
    • Related Report
      2009 Annual Research Report
  • [Presentation] 単純並列化によるマルチカノニカル分子動力学法のサンプリング効率の向上2009

    • Author(s)
      中村春木
    • Organizer
      第47回日本生物物理学会年会
    • Place of Presentation
      アスティとくしま、徳島
    • Year and Date
      2009-10-30
    • Related Report
      2009 Annual Research Report
  • [Presentation] ポルフィリン側鎖のヘムの電子構造への影響に関する理論的研究2009

    • Author(s)
      中村春木
    • Organizer
      第47回日本生物物理学会年会
    • Place of Presentation
      アスティとくしま、徳島
    • Year and Date
      2009-10-30
    • Related Report
      2009 Annual Research Report
  • [Presentation] Protein Function Annotation from Sequences and Structures with Tools at PDBj2009

    • Author(s)
      Haruki Nakamura
    • Organizer
      AsCA'09
    • Place of Presentation
      Jingyi Hotel, Beijing,中国
    • Year and Date
      2009-10-24
    • Related Report
      2009 Annual Research Report
  • [Presentation] Structural modeling of proteins : Principle and application to an ion channel2009

    • Author(s)
      Haruki Nakamura
    • Organizer
      The 36th Congress of the International Union of Physiological Sciences
    • Place of Presentation
      国立京都国際会館、京都
    • Year and Date
      2009-07-29
    • Related Report
      2009 Annual Research Report
  • [Presentation] 蛋白質構造データバンク事業と国際的な展開2009

    • Author(s)
      中村春木
    • Organizer
      統合データベースプロジェクト「データベースが拓くこれからのライフサイエンス」
    • Place of Presentation
      東京大学武田ホール、東京
    • Year and Date
      2009-06-12
    • Related Report
      2009 Annual Research Report
  • [Presentation] 光合成反応中心の色素配置に関する理論研究2009

    • Author(s)
      中村春木
    • Organizer
      第9回日本蛋白質科学会年会
    • Place of Presentation
      熊本全日空ホテルニュースカイ、熊本
    • Year and Date
      2009-05-22
    • Related Report
      2009 Annual Research Report
  • [Presentation] 基準振動に基づく蛋白質複合体界面の動的構造の解析2009

    • Author(s)
      木下賢吾
    • Organizer
      第9回日本蛋白質科学会年会
    • Place of Presentation
      熊本全日空ホテルニュースカイ、能本
    • Year and Date
      2009-05-21
    • Related Report
      2009 Annual Research Report
  • [Presentation] マルチカノニカル分子動力学シミュレーションによる57残基蛋白質の天然構造の再現2009

    • Author(s)
      中村春木
    • Organizer
      第9回日本蛋白質科学会年会
    • Place of Presentation
      熊本全日空ホテルニュースカイ、熊本
    • Year and Date
      2009-05-21
    • Related Report
      2009 Annual Research Report
  • [Presentation] シミュレーションとデータベース検索によるヒトラミニレ活性発現のために重要な立体構造の検討2009

    • Author(s)
      中村春木
    • Organizer
      第9回日本蛋白質科学会年会
    • Place of Presentation
      熊本全日空ホテルニュースカイ、熊本
    • Year and Date
      2009-05-21
    • Related Report
      2009 Annual Research Report
  • [Presentation] 粗視化モデルを用いた全原子モデルの効率化2009

    • Author(s)
      中村春木
    • Organizer
      第9回日本蛋白質科学会年会
    • Place of Presentation
      熊本全日空ホテルニュースカイ、熊本
    • Year and Date
      2009-05-21
    • Related Report
      2009 Annual Research Report
  • [Presentation] Ab initio QM/MDシミュレーションによるプロリンcis-trans異性化の自由エネルギー地形と水和の影響2009

    • Author(s)
      中村春木
    • Organizer
      第9回日本蛋白質科学会年会
    • Place of Presentation
      熊本全日空ホテルニュースカイ、熊本
    • Year and Date
      2009-05-21
    • Related Report
      2009 Annual Research Report
  • [Presentation] あらわな溶媒と膜分子モデルによるダイナミックな効果を取り入れた光合成活性中心の電子状態計算2009

    • Author(s)
      中村春木
    • Organizer
      第9回日本蛋白質科学会年会
    • Place of Presentation
      熊本全日空ホテルニュースカイ、熊本
    • Year and Date
      2009-05-21
    • Related Report
      2009 Annual Research Report
  • [Presentation] シトクロムc酸化酵素CuAサイトの電子状態解析2009

    • Author(s)
      中村春木
    • Organizer
      第9回日本蛋白質科学会年会
    • Place of Presentation
      熊本全日空ホテルニュースカイ、熊本
    • Year and Date
      2009-05-21
    • Related Report
      2009 Annual Research Report
  • [Presentation] ヘムエリスリンの活性中心の電子構造への蛋白場の影響2009

    • Author(s)
      中村春木
    • Organizer
      第9回日本蛋白質科学会年会
    • Place of Presentation
      熊本全日空ホテルニュースカイ、熊本
    • Year and Date
      2009-05-21
    • Related Report
      2009 Annual Research Report
  • [Presentation] Protein Functional Annotation from Structures2009

    • Author(s)
      Haruki Nakamura
    • Organizer
      NEDO International Symposium
    • Place of Presentation
      The Univ. Tokyo (Japan)
    • Year and Date
      2009-01-26
    • Related Report
      2008 Annual Research Report
  • [Presentation] Web services for function prediction of proteins2009

    • Author(s)
      Kengo Kinoshita
    • Organizer
      Bioinfo2009
    • Place of Presentation
      韓国・釜山
    • Related Report
      2009 Annual Research Report
  • [Presentation] Pattern recognition for protein 3D structures2008

    • Author(s)
      中村春木
    • Organizer
      情報処理学会バイオ情報学研究会
    • Place of Presentation
      大阪大学(豊中・大阪)
    • Year and Date
      2008-12-18
    • Related Report
      2008 Annual Research Report
  • [Presentation] リゾチーム周辺における水分子の流れパターン(順流、渦流、Dry/Wet流れ)に関する分子シミュレーションによる解析2008

    • Author(s)
      中村春木
    • Organizer
      第46回日本生物物理学会年会
    • Place of Presentation
      福岡国際会議場(福岡)
    • Year and Date
      2008-12-05
    • Related Report
      2008 Annual Research Report
  • [Presentation] ヘテロタイマーの多様性 : 蛋白質複合体構造予測の研究から得られた知見2008

    • Author(s)
      中村春木
    • Organizer
      第46回日本生物物理学会年会
    • Place of Presentation
      福岡国際会議場(福岡)
    • Year and Date
      2008-12-04
    • Related Report
      2008 Annual Research Report
  • [Presentation] 抗体カノニカル構造再訪2008

    • Author(s)
      中村春木
    • Organizer
      第46回日本生物物理学会年会
    • Place of Presentation
      福岡国際会議場(福岡)
    • Year and Date
      2008-12-04
    • Related Report
      2008 Annual Research Report
  • [Presentation] PiRaNha : 蛋白質配列からのRNA結合残基予測2008

    • Author(s)
      中村春木
    • Organizer
      第46回日本生物物理学会年会
    • Place of Presentation
      福岡国際会議場(福岡)
    • Year and Date
      2008-12-04
    • Related Report
      2008 Annual Research Report
  • [Presentation] マルチカノニカル分子動力学シミュレーションによる57残基蛋白質の構造探索2008

    • Author(s)
      冲村春木
    • Organizer
      第46回日本生物物理学会年会
    • Place of Presentation
      福岡国際会議場(福岡)
    • Year and Date
      2008-12-03
    • Related Report
      2008 Annual Research Report
  • [Presentation] 粗視化モデルを用いた全原子シミュレーションの効率化2008

    • Author(s)
      中村春木
    • Organizer
      第46回日本生物物理学会年会
    • Place of Presentation
      福岡国際会議場(福岡)
    • Year and Date
      2008-12-03
    • Related Report
      2008 Annual Research Report
  • [Presentation] IG-Base : immunoglobulin structural database for antibody engineenng2008

    • Author(s)
      Haruki Nakamura
    • Organizer
      The 3^<rd> MEI International Symposium
    • Place of Presentation
      Hyatt Regency San-FranciSCO(U.S.A.)
    • Year and Date
      2008-12-02
    • Related Report
      2008 Annual Research Report
  • [Presentation] Standardization, Validation and Integration of Protein 3D Structure Information2008

    • Author(s)
      Haruki Nakamura
    • Organizer
      4'th International Symposium on StandardReference Data
    • Place of Presentation
      Daejeon Convention Center, Daejeon (Korea)
    • Year and Date
      2008-10-28
    • Related Report
      2008 Annual Research Report
  • [Presentation] PiRaNhA : A Server for the Prediction of RNA-binding Residues in Protein Sequences2008

    • Author(s)
      Haruki Nakamura
    • Organizer
      International Conference on Bioinformatics, 2008
    • Place of Presentation
      National Yang Ming University (Taiwan)
    • Year and Date
      2008-10-20
    • Related Report
      2008 Annual Research Report
  • [Presentation] Protein functional annotation from pattern recognition for 3D structures.2008

    • Author(s)
      中村春木
    • Organizer
      Pattern Recognition in Bioinformatics 2008
    • Place of Presentation
      Novotel St Kilda, Melbourne(Australia)
    • Year and Date
      2008-10-15
    • Related Report
      2010 Final Research Report
  • [Presentation] Protein functional annotation from pattern recognition for 3Dstructures2008

    • Author(s)
      Haruki Nakamura
    • Organizer
      Pattern Recognition in Bioinformatics 2008
    • Place of Presentation
      Novotel St Kilda, Melbourne (Australia)
    • Year and Date
      2008-10-15
    • Related Report
      2008 Annual Research Report
  • [Presentation] Development of scoring functions for predicting protein complex structures2008

    • Author(s)
      Haruki Nakamura
    • Organizer
      Japan-UK Symposium on Protein InformaticS toward Interactome Analysis
    • Place of Presentation
      千里ライフサイエンスセンター(大阪)
    • Year and Date
      2008-09-01
    • Related Report
      2008 Annual Research Report
  • [Presentation] H3-rules, Progress report 20072008

    • Author(s)
      Haruki Nakamura
    • Organizer
      2^<nd> Pacific Rim International Conference on Protein Science
    • Place of Presentation
      Cairns Convention Centre, Australia
    • Year and Date
      2008-06-23
    • Related Report
      2008 Annual Research Report
  • [Presentation] Assembly simulation of four peptide chains in explicit waterby multicanonical molecular dynamics2008

    • Author(s)
      Haruki Nakamura
    • Organizer
      2^<nd> Pacific Rim International Conference on Protein Science
    • Place of Presentation
      Cairns Convention Centre, Australia
    • Year and Date
      2008-06-23
    • Related Report
      2008 Annual Research Report
  • [Presentation] Development of a scoring method for predicting protein complex structures2008

    • Author(s)
      Haruki Nakamura
    • Organizer
      2^<nd> Pacific Rim International Conference on Protein Science
    • Place of Presentation
      Cairns Convention Centre, Australia
    • Year and Date
      2008-06-23
    • Related Report
      2008 Annual Research Report
  • [Presentation] 抗体相補性決定領域の網羅的構造分類2008

    • Author(s)
      中村春木
    • Organizer
      第8回日本蛋白質科学会年会
    • Place of Presentation
      タワーホール船堀(東京)
    • Year and Date
      2008-06-10
    • Related Report
      2008 Annual Research Report
  • [Presentation] Flexible protein-protein docking by Monte Carlo plus Minimization of an all-atom field2008

    • Author(s)
      中村春木
    • Organizer
      第8回日本蛋白質科学会年会
    • Place of Presentation
      タワーホール船堀(東京)
    • Year and Date
      2008-06-10
    • Related Report
      2008 Annual Research Report
  • [Presentation] マルチカノニカル分子動力学法によるアミロイドペプチド4本鎖の会合シミュレーション2008

    • Author(s)
      中村春木
    • Organizer
      第8回日本蛋白質科学会年会
    • Place of Presentation
      タワーホール船堀(東京)
    • Year and Date
      2008-06-10
    • Related Report
      2008 Annual Research Report
  • [Presentation] アルファ/ベーダ両二次構造を含む40残基蛋白質の立体構造サンプリング2008

    • Author(s)
      中村春木
    • Organizer
      第8回日本蛋白質科学会年会
    • Place of Presentation
      タワーホール船堀(東京)
    • Year and Date
      2008-06-10
    • Related Report
      2008 Annual Research Report
  • [Presentation] 蛋白質周辺における水の協調的な流れの分子動力学シミュレーションによる解析2008

    • Author(s)
      中村春木
    • Organizer
      第8回日本蛋白質科学会年会
    • Place of Presentation
      タワーホール船堀(東京)
    • Year and Date
      2008-06-10
    • Related Report
      2008 Annual Research Report
  • [Presentation] 蛋白質複合体構造予測のための評価法の開発2008

    • Author(s)
      中村春木
    • Organizer
      第8回日本蛋白質科学会年会
    • Place of Presentation
      タワーホール船堀(東京)
    • Year and Date
      2008-06-10
    • Related Report
      2008 Annual Research Report
  • [Book] タンパク質計算科学2009

    • Author(s)
      神谷成敏・肥後順一・福西快文・中村春木
    • Total Pages
      251
    • Publisher
      共立出版
    • Related Report
      2010 Final Research Report 2009 Annual Research Report
  • [Book] やさしい原理からはいるタンパク質科学実験法:タンパク質のはたらきを知る-分子機能と生体作用-(「タンパク質のデータベースとインフォマティクス」)(長谷・高尾・高木編)第7章2009

    • Author(s)
      中村春木
    • Publisher
      化学同人
    • Related Report
      2010 Final Research Report
  • [Book] やさしい原理からはいるタンパク質科学実験法:タンパク質のはたらきを知る・分子機能と生体作用・(長谷・高尾・高木編)2009

    • Author(s)
      中村春木
    • Total Pages
      171
    • Publisher
      化学同人
    • Related Report
      2009 Annual Research Report
  • [Book] Prediction of molecular interactions from 3D-structures : from small ligands to large protein complexes(Janusz Bujnicki ed.)2008

    • Author(s)
      K. Kinoshita, H. Kono, K. Yura
    • Publisher
      Wiley & Sons
    • Related Report
      2010 Final Research Report
  • [Book] Prediction of molecular interactions from 3D-structures : from small ligandsto large protein complexes2008

    • Author(s)
      Kengo Kinoshita
    • Publisher
      Wiley and Sons
    • Related Report
      2008 Annual Research Report
  • [Remarks] ホームページ

    • Related Report
      2010 Final Research Report
  • [Remarks] HINTdb

    • URL

      http://hintdb.hgc.jp/hint/

    • Related Report
      2010 Final Research Report
  • [Remarks] HitPredict

    • URL

      http://hintdb.hgc.jp/htp/

    • Related Report
      2010 Final Research Report
  • [Remarks] COXPRESdb

    • URL

      http://coxpresdb.jp/

    • Related Report
      2010 Final Research Report
  • [Remarks] ATTED-II

    • URL

      http://atted.jp/

    • Related Report
      2010 Final Research Report
  • [Remarks]

    • URL

      http://hintdb.hgc.jp/htp/

    • Related Report
      2010 Annual Research Report
  • [Remarks]

    • URL

      http://hintdb/hgc.jp/hint/

    • Related Report
      2010 Annual Research Report
  • [Remarks]

    • URL

      http://coxpresdb.jp

    • Related Report
      2010 Annual Research Report

URL: 

Published: 2008-04-01   Modified: 2016-04-21  

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