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主な原著論文
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
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
主な原著論文
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
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
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
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
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
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
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
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
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
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
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
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
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)
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
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
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
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
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
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
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
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
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
- 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
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
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
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
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
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
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
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
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 KitauraBinding Affinity Prediction of Adenosine Deaminase Inhibitors by Linear Interaction Energy Method: Atomic Partial Charges around the Zinc Ion
Takahiro Kosugi, Isao Nakanishi and Kazuo KitauraHomology 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 KitauraThe 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 KitauraApplication 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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