業績リスト
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学会発表・受賞等

主な原著論文

  1. I. Nakanishi, D.G. Fedrov and K. Kitaura
    Molecular recognition mechanism of FK506 binding protein: An electron fragment molecular orbital study.
    Proteins: Struct. Funct. Bioinformatics, 2007, in press

  2. S. Nakamura, I Nakanishi and K. Kitaura
    Binding affinity prediction of non-peptide inhibitors of HIV-1 protease using COMBINE model introduced from peptide inhibitors
    Bioorg. Med. Chem. Lett., 2006, 16, 6334-6337

過去に発表した研究関連の論文

　　FMO関連 　　SBDD関連 　　生体高分子シミュレーション関連

主な原著論文

FMO関連

  1. Y. Mochizuki, S. Koikegami, T. Nakano, S. Amari, and K. Kitaura
    Large scale MP2 calculations with fragment molecular orbital scheme
    Chem. Phys. Lett., 2004, 396, 473-479

  2. D.G. Fedorov and K. Kitaura
    Second order Moller-Plesset perturbation theory based upon the fragment molecular orbital method (FMO)
    J. Chem. Phys., 2004, 121, 2483-2490

  3. D.G. Fedorov and K. Kitaura
    On the accuracy of the 3-body fragment molecular orbital method (FMO) applied to density functional theory
    Chem. Phys. Lett., 2004, 389, 129-134

  4. D.G. Fedorov and K. Kitaura
    The importance of three-body terms in the fragment molecular orbital method
    J. Chem. Phys., 2004, 120, 6832-6840

  5. D.G..Fedorov, R.M. Olson, K. Kitaura, M.S. Gordon, and S. Koseki
    A new hierarchical parallelization scheme: generalized distributed data interface (GDDI), and an application to the fragment molecular orbital method (FMO)
    J. Comp. Chem., 2004, 25, 872-880

  6. Y. Komeiji, T. Nakano, K. Fukuzawa, Y. Ueno, Y. Inadomi, T. Nemoto, M. Uebayasi, D. G. Fedorov and K. Kitaura
    Fragment molecular orbital method: application to molecular dynamics simulation, 'ab initio FMO-MD'
    Chem. Phys. Lett., 2003, 372, 342-347

  7. K. Nagayoshi, T. Ikeda, K. Kitaura and S. Nagase
    Computational procedure of lattice energy using the ab initio MO method
    J. Theoret. Comput. Chem., 2003, 2, 233-244

  8. T. Ikeda, K. Nagayoshi and K. Kitaura
    Ab initio MO based lattice energy for molecular crystals: packing structure of electron donor-acceptor (EDA) complex H3N-BF3
    Chem. Phys. Lett., 2003, 370, 218-226

  9. K. Nagayoshi, K. Kitaura, S. Koseki, S. Re, K. Kobayashi, Y-K. Choe and S. Nagase
    Calculation of packing structure of methanol solid using ab initio lattice energy at the MP2 level
    Chem. Phys. Lett., 2003, 369, 597-607

  10. Y. Inadomi, T. Nakano, K. Kitaura and U. Nagashima
    Definition of molecular orbitals in fragment molecular orbital method
    Chem. Phys. Lett., 2002, 364, 139-143

  11. T. Nakano, T. Kaminuma, T. Sato, K. Fukuzawa, Y. Akiyama, M.Uebayasi and K. Kitaura
    Fragment molecular orbital method: use of approximate electrostatic potential
    Chem. Phys. Lett., 2002, 351, 475-480

  12. K. Kitaura, S. Sugiki, T. Nakano, Y. Komeiji and M. Uebayasi
    Fragment molecular orbital method: analytical energy gradients
    Chem. Phys. Lett., 2001, 336, 163-170

  13. T. Sato, Y. Akiyama, T. Nakano, M. Uebayasi, and K. Kitaura
    Evaluation of parallel efficiency of ABINIT-MP program for ab initio fragment MO method
    High performance computing system, 2000, 41, 104-112 (in Japanese)

  14. T. Nakano, T. Kaminuma, T. Sato, Y. Akiyama, M. Uebayasi and K. Kitaura
    Fragment molecular orbital method: application to polypeptides
    Chem. Phys. Lett., 2000, 318, 614-618

SBDD関連

  1. T. Terasaka, T. Kinoshita, M. Kuno, N. Seki, K. Tanaka and I. Nakanishi
    Structure-based design, synthesis, and structure-activity relationship studies of novel non-nucleoside adenosine deaminase inhibitors
    J. Med. Chem., 2004, 47, 3730-3743

  2. T. Terasaka, H. Okumura, K. Tsuji, T. Kato, I. Nakanishi, T.Kinoshita, Y. Kato, M. Kuno, N. Seki, Y. Naoe, T. Inoue, K. Tanaka, K.Nakamura
    Structure-based design and synthesis of non-nucleoside, potent and orally bioavailable adenosine deaminase inhibitors
    J. Med. Chem., 2004, 47, 2728-2731

  3. T. Kinoshita, I. Nakanishi, M. Warizaya, A. Iwashita, Y. Kido, K.Hattori and T. Fujii
    Inhibitor-induced structural change of the active site of humanpoly(ADP-ribose) polymerase
    FEBS Letters, 2004, 556, 43-46

  4. T. Terasaka, T. Kinoshita, M. Kuno and I. Nakanishi
    A highly potent non-nucleoside adenosine deaminase inhibitor: Efficient drug discovery by intentional lead hybridization
    J. Am. Chem. Soc., 2004, 126, 34-35

  5. T. Terasaka, I. Nakanishi, K. Nakamura, Y. Eikyu, T. Kinoshita, N.Nishio, A. Sato, M. Kuno, N. Seki and K. Sakane
    Structure-based de novo design of non-nucleoside adenosine deaminase inhibitors
    Bioorg. Med. Chem. Lett., 2003, 13, 1115−1118

  6. T. Kinoshita, N. Nishio, I. Nakanishi, A. Sato and T. Fujii
    Structure of bovine adenosine deaminase complexed with 6-hydroxy-1,6 dihydropurine riboside
    Acta Cryst. Section D: Biological Crystallography, 2003, 59, 299-303

  7. T. Kinoshita, I. Nakanishi, A. Sato and T. Tada
    True interaction mode of porcine pancreatic elastase with FR136706, a potent peptidyl inhibitor
    Bioorg. Med. Chem. Lett., 2003, 13, 21-24

  8. K. Tomita, K. Suzuki, H. Ohishi and I. Nakanishi
    Molecular structure and mutual recognition between host and guest molecules found in the crystal structures of oxacalix[4]arenes complexed with xylene isomers
    J. Inc. Phenom. Mol. Recog. Chem., 2000, 37, 341-357

    10. I. Nakanishi, T. Kinoshita, A. Sato and T. Tada
    Structure of porcine pancreatic elastase complexed with FR901277, a novel macrocyclic inhibitor of elastase, at 1.6 A resolution
    Biopolymers, 2000, 53, 434-445

  10. I. Nakanishi, A. Fujikawa, K. Imai and A. Sato
    1H-NMR determination of the solution structure and absolute configuration of FR134043, a novel inhibitor of human leukocyte elastase
    J. Peptide Res., 2000, 55, 120-128

生体高分子シミュレーション関連

  1. K. Murata, Y. Sugita, and Y. Okamoto
    Molecular dynamics simulations of DNA dimers based on replica-exchange umbrella sampling. I. Test of sampling efficiency
    J. Theor. Comput. Chem., 2005, 4, 411-432

  2. K. Murata, Y. Sugita, and Y. Okamoto
    Molecular dynamics simulations of DNA dimers based on replica-exchange umbrella sampling. II. Free energy analysis
    J. Theor. Comput. Chem., 2005, 4, 433-448

  3. K. Murata, Y. Sugita, and Y. Okamoto
    Free energy calculations for DNA base stacking by replica-exchange umbrella sampling
    Chem. Phys. Lett., 2004, 85, 1-7

  4. K. Murata, T. Hoshino, Y. Sato, M. Hata, M. Tsuda
    Unidirectional proton transfer mechanism in the L→M→N sequence of bacteriorhodopsin.
    J. Mol. Struct. (Theochem), 2003, 664-665, 125-133

  5. K. Murata, T. Hoshino, Y. Sato, M. Hata, and M. Tsuda
    A factor to determine the direction of the proton transfer in bacteriorhodopsin.
    Chem-Bio Info. J., 2002, 2, 95-101

  6. K. Murata, Y. Fujii, N. Enomoto, M. Hata, T. Hoshino, and M. Tsuda
    A Study on the Mechanism of the Proton Transfer in Bacteriorhodopsin : The Importance of the Water Molecule.
    Biophys. J., 2000, 79, 982-991

学会発表

分子構造総合討論会2004 (2004年・広島)

  • FMOによるFKBPとリガンドの相互作用解析
    　村田 克美, 仲西 功, Dmitri G. Fedorov, 北浦 和夫

    • 第1回NAREGI国際会議 (2005年・奈良)

  • A swap model to predict binding affinities of host-guest complexes
    　Katsumi Murata, Isao Nakanishi and Kazuo Kitaura

    • 第7回薬物の分子設計と開発に関する日中合同シンポジウム (2005年・杭州＠中国)

  • COMBINE analysis predicts binding affinities of ligands with a new scaffold
    　Shinya Nakamura, Isao Nakanishi and Kazuo Kitaura
  • Binding Affinity Prediction of Adenosine Deaminase Inhibitors by Linear Interaction Energy Method: Atomic Partial Charges around the Zinc Ion
    　Takahiro Kosugi, Isao Nakanishi and Kazuo Kitaura
  • Homology Modeling of hCRM1/Exportin1 by Fold Recognition Method
    　Naoya Nagata, Satoru Tamura, Atsushi Shiomi, Nobutoshi Murakami, Isao Nakanishi and Kazuo Kitaura

    • 第33回構造活性相関シンポジウム (2005年・大阪)

  • COMBINE解析法の新規骨格探索への応用：HIV-1 protease 阻害剤への適用
    　中村 真也, 仲西 功, 北浦 和夫
  • hCRM1/Exportin1のホモロジーモデリングとドッキングスタディ
    　永田 尚也, 田村 理, 塩見 敦, 村上 啓寿, 仲西 功, 北浦 和夫

    • 第28回情報化学討論会 (2005年・大阪)

  • 内部エネルギーを考慮したLinear Response 理論に基づく結合エネルギーの予測
    　小杉 貴洋, 仲西 功, 北浦 和夫

    • 第43回日本生物物理学会年会(2005年・北海道)

  • Adenosine Deaminase 阻害剤の結合エネルギーと結合モードの理論的予測
    　小杉 貴洋, 仲西 功, 北浦 和夫
  • 蛋白質のab initio フラグメントMO計算：FKBP‐リガンド複合体の相互作用と構造活性相関
    　仲西 功, Dmitri G. Fedorov, 北浦 和夫

    • 第19回分子シミュレーション討論会(2005年・愛知)

  • Linear Response 近似を用いた結合エネルギーの予測
    　小杉 貴洋, 仲西 功, 北浦 和夫

    • PACIFICHEM 2005(2005年・ハワイ＠米国)

  • Calculation of the protein-ligand binding energies using a swapping model
    　Katsumi Murata, Isao Nakanishi and Kazuo Kitaura

    • 第125回日本薬学会年会(2006年・仙台)

  • COMBINE 解析を用いたリガンドの結合モード予測
    　永田 尚也, 中村 真也, 仲西 功, 北浦 和夫
  • Fragment MO法を用いたHIVプロテアーゼ阻害剤の活性評価
    　中村 真也, 仲西 功, 北浦 和夫
  • Comparative binding energy 解析法によるPARP 阻害剤の活性予測
    　横田 彰宏, 中村 真也, 仲西 功, 北浦 和夫

    • Symposium on Progress and Future Prospects in Molecular Dynamics Simulation -In Memory of Professor Shuichi Nose-(2006年・横浜)

  • A swap model to predict binding affinities of protein-ligand complexes
    　Katsumi Murata, Isao Nakanishi and Kazuo Kitaura

    • The 16th European Symposium on Quantitative Structure-Activity Relationships & Molecular Modelling(2006年・ローマ＠イタリア)

  • Computational elucidation of compound selectivity of adenosine deaminase: Affinities to EHNA and THNA enantiomers
    　Takahiro Kosugi, Isao Nakanishi and Kazuo Kitaura
  • Application of COMBINE analysis to virtual screening: Verification in scoring function for docking pose prediction
    　Shinya Nakamura, Naoya Nagata, Isao Nakanishi and Kazuo Kitaura

    • 第34回構造活性相関シンポジウム (2006年・新潟)

  • ADA阻害剤のmethyl基導入に伴うダイナミクスと結合エネルギーの変化
    　小杉 貴洋, 仲西 功, 北浦 和夫
  • リガンド結合部位に存在する水分子との競合を考慮したCOMBINE解析
    　横田 彰宏, 中村 真也, 仲西 功, 北浦 和夫

    • Fifth East Asian Biophysics Symposium & Forty-Fourth Annual Meeting of the Biophysical Society of Japan (2006年・沖縄)

  • Prediction of hydrogen-bonding sites between Protein and Ligand by Molecular Dynamics Simulation
    　Katsumi Murata, Naoya Nagata, Isao Nakanishi and Kazuo Kitaura

    • 受賞

  • 日本薬学会構造活性相関部会 SAR Promotion Award：中村真也
  • 第28回情報化学討論会 ポスター賞：小杉貴洋
  • 第34回構造活性相関シンポジウム ポスター賞：横田彰宏


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