"北尾彰朗","Conformational Change and Dissociation/Association of Biological Macromolecules Investigated by Parallel Cascade Selection Molecular Dynamics and Markov State Model","ABA, APPA &TBS Joint Congress",,,,,,2023,June
"Akio Kitao","Molecular Simulation to Investigate Open?Close Motion of a Flagellar Export Apparatus Protein FlhAC",,"Methods in Molecular Biology",,,,"pp. 27-34",2023,Feb.
"Mariko Kojima,Satoshi Abe,Tadaomi Furuta,Duy Phuoc Tran,Kunio Hirata,Keitaro Yamashita,Yuki Hishikawa,Akio Kitao,Takafumi Ueno","Engineering of an in-cell protein crystal for fastening a metastable conformation of a target miniprotein",,"Biomater. Sci.",,"vol. 11","no. 4","pp. 1350-1357",2023,Feb.
"Tatsuro Nishikino,Norihiro Takekawa,Duy Phuoc Tran,Jun-ichi Kishikawa,Mika Hirose,Sakura Onoe,Seiji Kojima,Michio Homma,Akio Kitao,Takayuki Kato,Katsumi Imada","Structure of MotA, a flagellar stator protein, from hyperthermophile",,"Biochemical and Biophysical Research Communications",,,,,2022,Nov.
"中矢光,TranPhuoc Duy,北尾彰朗","並列カスケード選択分子動力学法を用いた生体分子の解離過程解析","第16回分子科学討論会",,,,,,2022,Sept.
"Kazuhiro Takemura,Akio Kitao","Molecular dynamics",,"Plasma Membrane Shaping",,,,"pp. 431-443",2022,Sept.
"Akio Kitao","Conserved GYXLI Motif of FlhA Is Involved in Dynamic Domain Motions of FlhA Required for Flagellar Protein Export",,"Microbiology Spectrum",,,,,2022,July
"Akio Kitao","Principal Component Analysis and Related Methods for Investigating the Dynamics of Biological Macromolecules",,"J",,,,,2022,June
"Satoshi Yamashita,Misao Mizuno,Kazuhiro Takemura,Akio Kitao,Yasuhisa Mizutani","Dependence of Vibrational Energy Transfer on Distance in a Four-Helix Bundle Protein: Equidistant Increments with the Periodicity of α Helices",,"The Journal of Physical Chemistry B",,,,,2022,May
"Akio Kitao","Dissociation Pathways of the p53 DNA Binding Domain from DNA and Critical Roles of Key Residues Elucidated by dPaCS-MD/MSM",,"Journal of Chemical Information and Modeling",,,,,2022,Mar.
"Duy Phuoc Tran,Yuta Taira,Takumi Ogawa,Ryoga Misu,Yoshiki Miyazawa,Akio Kitao","Inhibition of the hexamerization of SARS-CoV-2 endoribonuclease and modeling of RNA structures bound to the hexamer",,"Scientific Reports",,,,,2022,Mar.
"Mariko Kojima,Yuki Hishikawa,Satoshi Abe,Tadaomi Furuta,Duy Phuoc Tran,Akio Kitao,Takafumi Ueno","Dynamics structural analysis of  miniprotein by in-cell crystal engineering","The 102nd CSJ Annual Meeting (2022)",,,,,,2022,Mar.
"Darin Flamandita,Akio Kitao","Substrate Unbinding Pathways from Candida rugosa Lipase Investigated by Parallel Cascade Selections Molecular Dynamics and the Markov State Model","第11回日本生物物理学会関東支部会",,,,,,2022,Mar.
"Hiroaki Hata,Duy Phuoc Tran,Marzouk,Akio Kitao","Binding free energy of protein/ligand complexes calculated using dissociation Parallel Cascade Selection Molecular Dynamics and Markov state model",,"Biophysics and Physicobiology",,,,,2021,Dec.
"Akio Kitao","Transport mechanisms of ions, peptides and proteins through the biological membrane","Pacific Basin Societies 2021",,,,,,2021,Dec.
"Steven Hayward,Akio Kitao","The role of the half-turn in determining structures of Alzheimer’s Aβ wild-type and mutants",,"Journal of Structural Biology",,"Vol. 213","No. 4","pp. 107792",2021,Dec.
"Akio Kitao","Roles of hydration/dehydration for dissociation, association and stabilization of protein complexes","Pacific Basin Societies 2021",,,,,,2021,Dec.
"Akio Kitao","Molecular movie of protein association/dissociation dynamics","59th Annual Meeting of Biophysical Society of Japan",,,,,,2021,Nov.
"Duy Phuoc Tran,Akio Kitao","Calculation of Binding Free Energy and Kinetic Rates with Flexible Protein Docking",,"Seibutsu Butsuri",,"Vol. 61","No. 6","pp. 398-399",2021,Nov.
"Kazuhiro Takemura,Akio Kitao","Unguided Binding MD of Protein-Protein Complexes by PPI-ColDock","59th Annual Meeting of Biophysical Society of Japan",,,,,,2021,Nov.
"Duy Tran,Akio Kitao","DNA bending enhances the dissociation of tetrameric p53’s coredomains","59th Annual Meeting of Biophysical Society of Japan",,,,,,2021,Nov.
"Ryunosuke Kiuchi,Kazuhiro Takemura,Akio Kitao","Application of ColDock to docking of cryptic pockets","59th Annual Meeting of Biophysical Society of Japan",,,,,,2021,Nov.
"Akio Kitao","PaCS-MD/MSM to investigate protein motions and association/dissociation of protein complexes","Symposium on Computer Simulations and Cryo-ET/EM of Complex Biomolecular Systems",,,,,,2021,Nov.
"Duy Phuoc Tran,Akio Kitao","Binding free energy calculation with dPaCS-MD/MSM","C2C Program Kick off symposium",,,,,,2021,Oct.
"Duy Phuoc Tran,Akio Kitao","Atomic mechanism of the complete association of intrinsically disordered peptide to protein","XXXII IUPAP Conference on Computational Physics(CCP2021)",,,,,,2021,Aug.
"Akio Kitao","Simulated dissociation/association dynamics between proteins and other molecules","Telluride Science Research Center Workshop on Protein Dynamics",,,,,,2021,July
"Duy Tran,Akio Kitao","Predicting the complex conformations of protein/intrinsically disordered peptide complexes","The Protein Society-35th Anniversary Symposium",,,,,,2021,July
"宮澤 佳希,Tran Phuoc Duy,竹村 和浩,北尾 彰朗","Parallel Cascade Selection Molecular Dynamics/Markov State Model によるタンパク質?タンパク質複合体の結合親和性評価 (Evaluation of binding affinity for protein-protein complexes by Parallel Cascade Selection Molecular Dynamics/Markov State Model","第21回日本蛋白質科学会年会",,,,,,2021,June
"チャン フ ズイ,畑 宏明,中矢 光,北尾彰朗","Benchmarking the free energy calculation of PaCS-MD/MSM","第21回日本蛋白質科学会年会",,,,,,2021,June
"Takeo Yamawaki,Misao Mizuno,Haruto Ishikawa,Kazuhiro Takemura,Akio Kitao,Yoshitsugu Shiro,Yasuhisa Mizutani","Regulatory Switching by Concerted Motions on the Microsecond Time Scale of the Oxygen Sensor Protein FixL",,"The Journal of Physical Chemistry B",,"Vol. 125","No. 25","pp. 6847-6856",2021,June
"Wijaya Tegar N.,北尾彰朗","Dynamics of Close-Open State of CALB Obtained by Parallel Cascade Molecular Dynamics Simulation and The 2.Wijaya Tegar N.、北尾彰朗「Dynamics of Close-Open State of CALB Obtained by Parallel Cascade Molecular Dynamics Simulation and The Markov State Model","第21回日本蛋白質科学会年会",,,,,,2021,June
"北尾彰朗","インシリコシミュレーションで探るタンパク質複合体の結合親和性とキネティックス","構造活性フォーラム2021「次期スーパーコンピュータ「富岳」時代の計算創薬」",,,,,,2021,June
"Marzouk,Akio Kitao","Investigating the dissociation process and kinetic rates of DBD-p53/DNA complex by PaCS-MD and MSM","第21回日本蛋白質科学会年会",,,,,,2021,June
"竹村 和浩,北尾 彰朗","PPI-ColDock 法を用いた蛋白質‐ 蛋白質複合体形成","第21回日本蛋白質科学会年会",,,,,,2021,June
"Duy Phuoc Tran,Akio Kitao","Using molecular dynamics simulations to prioritize and understand AI-generated cell penetrating peptides",,"Scientific Reports",,"Vol. 11","No. 1",,2021,May
"北尾彰朗","SARS-CoV-2 エンドリボヌクレアーゼのオリゴマー化阻害",,,,,,,2021,Apr.
"Tegar Nurwahyu Wijaya,Akio Kitao","Dynamics of Close-Open State of Candida antarctica Lipase B Obtained by Parallel Cascade Molecular Dynamics Simulation and The Markov State Model","第10回日本生物物理学会関東支部会",,,,,,2021,Mar.
"Akio Kitao","Delineating the conformational landscape of the adenosine A<sub>2A</sub> receptor during G protein coupling.",,"Cell",,,,,2021,Mar.
"Mariko Kojima,Yuki Hishikawa,Satoshi Abe,Tadaomi Furuta,Duy Phuoc Tran,Akio Kitao,Takafumi Ueno","Energy Analysis of Miniprotein by in Vivo Protein Crystallization","日本化学会第101春季年会",,,,,,2021,Mar.
"北尾 彰朗","東京工業大学生命理工学院 北尾研究室",,"アンサンブル","分子シミュレーション学会","Vol. 23","No. 1","pp. 67-71",2021,Jan.
"Hiroaki Hata,Yasutaka Nishihara,Masayoshi Nishiyama,Yoshiyuki Sowa,Ikuro Kawagishi,Akio Kitao","High pressure inhibits signaling protein binding to the flagellar motor and bacterial chemotaxis through enhanced hydration",,"Scientific Reports",,"Vol. 10","No. 1",,2020,Dec.
"宮澤佳希,TranPhuoc Duy,竹村和浩,北尾彰朗","PaCS-MD/MSM を用いたタンパク質-タンパク質複合体の結合親和性評価","第34回分子シミュレーション討論会",,,,,,2020,Dec.
"尾川拓巳,TranPhuoc Duy,藤井 高志,難波 啓一,北尾彰朗","PaCS-MDによるアクトミオシンの結合解離予測","第34回分子シミュレーション討論会 オンライン学会",,,,,,2020,Dec.
"平悠太,TranPhuoc Duy,北尾彰朗","分子動力学計算によるp53-C 末端部位のDNA 結合機構の解明","第34回分子シミュレーション討論会",,,,,,2020,Dec.
"Aini Gusmira,Kazuhiro Takemura,Shin Yong Lee,Takehiko Inaba,Kyoko Hanawa-Suetsugu,Kayoko Oono-Yakura,Kazuma Yasuhara,Akio Kitao,Shiro Suetsugu","Regulation of caveolae through cholesterol-depletion-dependent tubulation mediated by PACSIN2",,"Journal of Cell Science",,,,,2020,Oct.
"Kazuhiro Takemura,Akio Kitao","Unguided Binding MD of Protein-Protein Complexes by PPI-ColDock",,,,,,,2020,Sept.
"平悠太,TranPhuoc Duy,北尾彰朗","分子動力学計算によるp53-C 末端部位のDNA 結合機構の解明",,,,,,,2020,Sept.
"Marzouk,Akio Kitao","Investigating the dissociation process of DBD-p53/DNA complex by PaCS-MD and MSM",,,,,,,2020,Sept.
"宮澤佳希,TranPhuoc Duy,竹村和浩,北尾彰朗","PaCS-MD/MSM を用いたタンパク質複合体の速度定数評価",,,,,,,2020,Sept.
"北尾彰朗","高速分子動画を補完する構造変化の自由エネルギー地形と経路・流量の解析","第二回新学術「高速分子動画」オンラインセミナー",,,,,,2020,Aug.
"北尾彰朗","SARS-CoV-2タンパク質のオリゴマー化を阻害する薬剤候補分子の探索",,,,,,,2020,Aug.
"Duy Phuoc Tran,Akio Kitao","Simulating the association/dissociation process of flexible protein complexes","第20回日本蛋白質科学会年会",,,,,,2020,July
"Yoshiki Miyazawa,Duy Phuoc Tran,Kazuhiro Takemura,Akio Kitao","Protein-protein complex dissociation simulated by Parallel Cascade Selection Molecular Dynamics","第20回日本蛋白質科学会年会",,,,,,2020,July
"Kazuhiro Takemura,Akio Kitao","Unguided Binding MD of Protein-Protein Complexes by PPI-ColDock","第20回日本蛋白質科学会年会",,,,,,2020,July
"Kenichiro Takaba,Duy Phuoc Tran,Akio Kitao","Edge expansion parallel cascade selection molecular dynamics simulation for investigating large-amplitude collective motions of proteins",,"The Journal of Chemical Physics",,,,,2020,June
"北尾 彰朗","バイオ分野での量子コンピュータへの期待",,"現代化学",,"Vol. 6",,"pp. 50-51",2020,June
"北尾彰朗","バイオ分野での量子コンピュータへの期待",,"現代化学、v6(No.591)、p50-51",,"Vol. 6","No. 591","p. 50-51",2020,June
"Duy Phuoc Tran,Hiroaki Hata,Takumi Ogawa,Yuta Taira,Akio Kitao","PaCS-MD/MSM: Parallel Cascade Selection Molecular Dynamic Simulation in Combination with Markov State Model as an Efficient non-Bias Sampling Method",,"分子シミュレーション学会誌アンサンブル",,"Vol. 22",,"  151-156",2020,Apr.
"Tran Duy Phuoc,Hata Hiroaki,Ogawa Takumi,Taira Yuta,Kitao Akio,北尾彰朗","最近の研究から PaCS-MD/MSM : Parallel Cascade Selection Molecular Dynamic Simulation in Combination with Markov State Model as an Efficient non-Bias Sampling Method",,"アンサンブル","分子シミュレーション学会","Vol. 22","No. 2","pp. 151-156",2020,Mar.
"北尾彰朗","長時間ダイナミクス法と 標的分子ネットワーク",,,,,,,2020,Feb.
"Kei Terayama,Ai Shinobu,Koji Tsuda,Kazuhiro Takemura,Akio Kitao","evERdock BAI: Machine-learning-guided selection of protein-protein complex structure",,"The Journal of Chemical Physics",,"  151",,"  215104",2019,Dec.
"Kazuhiro Takemura,Akio Kitao","More efficient screening of protein-protein complex model structures for reducing the number of candidates",,"Biophysics and Physicobiology",,"  16",,"  295-303",2019,Nov.
"Justin Chan,Hong-Rui Lin,Kazuhiro Takemura,Kai-Chun Chang,Yuan-Yu Chang,Yasumasa Joti,Akio Kitao,Lee-Wei Yang","An Efficient Timer and Sizer of Biomacromolecular Motions",,"Structure",,,,,2019,Nov.
"Kyoko Hanawa-Suetsugu,Yuzuru Itoh,Maisarah Ab Fatah,Tamako Nishimura,Kazuhiro Takemura,Kohei Takeshita,Satoru Kubota,Naoyuki Miyazaki,Wan Nurul Izzati Wan Mohamad Noor,Takehiko Inaba,Nhung Thi Hong Nguyen,Sayaka Hamada-Nakahara,Kayoko Oono-Yakura,Masashi Tachikawa,Kenji Iwasaki,Daisuke Kohda,Masaki Yamamoto,Akio Kitao,Atsushi Shimada,Shiro Suetsugu","Phagocytosis is mediated by two-dimensional assemblies of the F-BAR protein GAS7",,"Nature Communications",,"  10","  1","  1-13",2019,Nov.
"Yuichi Yokochi,Kazunori Sugiura,Kazuhiro Takemura,Keisuke Yoshida,Satoshi Hara,Ken-ichi Wakabayashi,Akio Kitao,Toru Hisabori","Impact of key residues within chloroplast thioredoxin-f on recognition for reduction and oxidation of target proteins",,"Journal of Biological Chemistry",,"  294","  46","  17437-17450",2019,Nov.
"Yasumasa Joti,Akio Kitao","Cancellation between auto- and mutual correlation contributions of protein/water dynamics in terahertz time-domain spectra",,"Biophysics and Physicobiology",,"  16",,"  240-247",2019,Nov.
"Yasuhiro Onoue,Masayo Iwaki,Ai Shinobu,Yasutaka Nishihara,Hiroto Iwatsuki,Hiroyuki Terashima,Akio Kitao,Hideki Kandori,Michio Homma","Essential ion binding residues for Na+ flow in stator complex of the Vibrio flagellar motor",,"Scientific Reports",,"  9","  1","  1-16",2019,Aug.
"Kento Shin,Duy Phuoc Tran,Kazuhiro Takemura,Akio Kitao,Kei Terayama,Koji Tsuda","Enhancing Biomolecular Sampling with Reinforcement Learning: A Tree Search Molecular Dynamics Simulation Method",,"ACS Omega",,"  4","  9","  13853-13862",2019,Aug.
"Hiroaki Hata,Masayoshi Nishiyama,Akio Kitao","Molecular dynamics simulation of proteins under high pressure: Structure, function and thermodynamics",,"Biochimica et Biophysica Acta (BBA) - General Subjects",,,,,2019,July
"Hiroshi Nakagawa,Yasumasa Joti,Akio Kitao,Osamu Yamamuro,Mikio Kataoka","Universality and Structural Implications of the Boson Peak in Proteins",,"Biophysical Journal",,"  117","  2","  229-238",2019,July
"Nick Matthews,Akio Kitao,Stephen Laycock,Steven Hayward","Haptic-Assisted Interactive Molecular Docking Incorporating Receptor Flexibility",,"Journal of Chemical Information and Modeling",,"  59","  6","  2900-2912",2019,June
"Yumi Inoue,Yuya Ogawa,Miki Kinoshita,Naoya Terahara,Masafumi Shimada,Noriyuki Kodera,Toshio Ando,Keiichi Namba,Akio Kitao,Katsumi Imada,Tohru Minamino","Structural Insights into the Substrate Specificity Switch Mechanism of the Type III Protein Export Apparatus",,"Structure",,"  27","  6","  965-976. e6",2019,June
"Steven Hayward,Akio Kitao","Multi-strand β-sheet of Alzheimer Aβ(1?40) folds to β-strip helix: implication for protofilament formation",,"Journal of Biomolecular Structure and Dynamics",,"  37","  8","pp. 2143-2153",2019,May
"Duy Phuoc Tran,Akio Kitao","Dissociation Process of a MDM2/p53 Complex Investigated by Parallel Cascade Selection Molecular Dynamics and the Markov State Model",,"The Journal of Physical Chemistry B",,"  123","  11","  2469-2478",2019,Mar.
"Ai Shinobu,Kazuhiro Takemura,Nobuyuki Matubayasi,Akio Kitao","Refining evERdock: Improved selection of good protein-protein complex models achieved by MD optimization and use of multiple conformations",,"The Journal of Chemical Physics",,"  149","  19","  195101",2018,Nov.
"Hisham M. Dokainish,Akio Kitao","Similarities and Differences between Thymine(6?4)Thymine/Cytosine DNA Lesion Repairs by Photolyases",,"The Journal of Physical Chemistry B",,"  122","  36","  8537-8547",2018,Aug.
"Kazuhiro Takemura,Chika Sato,Akio Kitao","ColDock: Concentrated Ligand Docking with All-Atom Molecular Dynamics Simulation",,"The Journal of Physical Chemistry B",,"  122","  29","  7191-7200",2018,July
"Mizuki Tabata,Hisham Dokainish,Keisuke Yamaguchi,Akio Kitao,Shun-ichi Ishiuchi,Masaaki Fujii","GAS PHASE SPECTROSCOPY ON HYDRATED CLUSTERS OF OXYTOCIN BY ELECTROSPRAY IONIZATION / COLD ION TRAP TECHNIQUE","International Symposium on Molecular Spectroscopy",,,,,,2018,June
"Satoshi Yamashita,Misao Mizuno,Duy Phuoc Tran,Hisham Dokainish,Akio Kitao,Yasuhisa Mizutani","Vibrational Energy Transfer from Heme through Atomic Contacts in Proteins",,"The Journal of Physical Chemistry B",,"Vol. 122","No. 22","pp. 5877-5884",2018,June
"Akio Kitao,Hiroaki Hata","Molecular dynamics simulation of bacterial flagella",,"Biophysical Reviews",,"  10","  2","  617-629",2018,Apr.
"Kazuhiro Takemura,Nobuyuki Matubayasi,Akio Kitao","Binding free energy analysis of protein-protein docking model structures by evERdock",,"The Journal of Chemical Physics",,"  148","  10","  105101",2018,Mar.
"Jacob B. Swadling,Akio Kitao","Origins of biological function in DNA and RNA hairpin loop motifs from replica exchange molecular dynamics simulation",,"Physical Chemistry Chemical Physics",,"Vol. 20","No. 5","pp. 2990-3001",2018,Feb.
"Duy Phuoc Tran,Akio Kitao","Protein-Ligand Dissociation Simulated by Parallel Cascade Selection Molecular Dynamics",,"Journal of Chemical Theory and Computation",,"Vol. 14","No. 1","pp. 404-417",2018,Jan.
"Kazuhiro Takemura,Kyoko Hanawa-Suetsugu,Shiro Suetsugu,Akio Kitao","Salt Bridge Formation between the I-BAR Domain and Lipids Increases Lipid Density and Membrane Curvature",,"Scientific Reports",,,,,2017,Dec.
"Nick Matthews,Robert Easdon,Akio Kitao,Steven Hayward,Stephen Laycock","High quality rendering of protein dynamics in space filling mode",,"Journal of Molecular Graphics & Modelling",,"Vol. 78",,"pp. 158-167",2017,Nov.
"Hisham M. Dokainish,Daichi Yamada,Tatsuya Iwata,Hideki Kandori,Akio Kitao","Electron Fate and Mutational Robustness in the Mechanism of (6-4)Photolyase-Mediated DNA Repair",,"ACS Catalysis",,,,"pp. 4835-4845",2017,July
"Akio Kitao,Nishihara, Yasutaka","Structure of the MotA/B Proton Channel.",,"Methods in molecular biology (Clifton, N.J.)",,"Vol. 1593",,"pp. 133-145",2017,Apr.
"Akio Kitao,Kazuhiro Takemura","High anisotropy and frustration: the keys to regulating protein function efficiently in crowded environments.",,"Current opinion in structural biology",,"Vol. 42",,"pp. 50-58",2017,Feb.
"Otani, Yuko,Watanabe, Satoshi,Ohwada, Tomohiko,Kitao, Akio,Akio Kitao","Molecular Dynamics Study of Nitrogen-Pyramidalized Bicyclic beta-Proline Oligomers: Length-Dependent Convergence to Organized Structures",,"Journal of Physical Chemistry B",,"Vol. 121","No. 1","pp. 100-109",2017,Jan.
"Dokainish, Hisham M.,Kitao, Akio,Akio Kitao","Computational Assignment of the Histidine Protonation State in (6-4) Photolyase Enzyme and Its Effect on the Protonation Step",,"Acs Catalysis",,"Vol. 6","No. 8","pp. 5500-5507",2016,Aug.
"Taguchi, Junko,Kitao, Akio,Akio Kitao","Dynamic profile analysis to characterize dynamics-driven allosteric sites in enzymes",,"Biophysics and Physicobiology",,"Vol. 13","No. 0","pp. 117-126",2016,Aug.
"Yamada, D.,Dokainish, H. M.,Iwata, T.,Yamamoto, J.,Ishikawa, T.,Todo, T.,Iwai, S.,Getzoff, E. D.,Kitao, A.,Kandori, H.,Akio Kitao","Functional Conversion of CPD and (6-4) Photolyases by Mutation",,"Biochemistry",,"Vol. 55","No. 30","pp. 4173-4183",2016,July
"Deguchi, A.,Tomita, T.,Ohto, U.,Kazuhiro Takemura,Akio Kitao,Miyake, K.,Akashi-Takamura, S.,Maru, Y.","Eritoran inhibits S100A8-mediated TLR4/MD-2 activation and tumor growth by changing the immune microenvironment",,"Oncogene",,"Vol. 35","No. 11","pp. 1445-1456",2016,
"Maru, Yoshiro,Tomita, Takeshi,Deguchi, Atsuko,Ieguchi, Katsuaki,Takita, Morichika,Tsukahara, Fujiko,Takemura, Kazuhiro,Kitao, Akio,Gusovsky, Fabian,Akio Kitao","Drug Targeting Based on a New Concept-Targeting Against TLR4 as an Example",,"Endocrine Metabolic & Immune Disorders-Drug Targets",,"Vol. 15","No. 2","pp. 83-87",2015,July
"Hayward, Steven,Kitao, Akio,Akio Kitao","Monte Carlo Sampling with Linear Inverse Kinematics for Simulation of Protein Flexible Regions",,"Journal of Chemical Theory and Computation",,"Vol. 11","No. 8","pp. 3895-3905",2015,
"Harada, Ryuhei,Kitao, Akio,Akio Kitao","Nontargeted Parallel Cascade Selection Molecular Dynamics for Enhancing the Conformational Sampling of Proteins",,"Journal of Chemical Theory and Computation",,"Vol. 11","No. 11","pp. 5493-5502",2015,
"Sakai, Taki,Matsumoto, Yotaro,Ishikawa, Minoru,Sugita, Kazuyuki,Hashimoto, Yuichi,Wakai, Nobuhiko,Kitao, Akio,Morishita, Era,Toyoshima, Chikashi,Hayashi, Tomoatsu,Akiyama, Tetsu,Akio Kitao","Design, synthesis and structure-activity relationship studies of novel sirtuin 2 (SIRT2) inhibitors with a benzamide skeleton",,"Bioorganic & Medicinal Chemistry",,"Vol. 23","No. 2","pp. 328-339",2015,
"Nishihara, Yasutaka,Kitao, Akio,Akio Kitao","Gate-controlled proton diffusion and protonation-induced ratchet motion in the stator of the bacterial flagellar motor",,"Proceedings of the National Academy of Sciences of the United States of America",,"Vol. 112","No. 25","pp. 7737-7742",2015,
"Wakai N,Takemura K,Morita T,Kitao A","Mechanism of Deep-Sea Fish α-Actin Pressure Tolerance Investigated by Molecular Dynamics Simulations.",,,,,,,2014,Jan.
"Takahashi, Nobuaki,Hamada-Nakahara, Sayaka,Itoh, Yuzuru,Takemura, Kazuhiro,Shimada, Atsushi,Ueda, Yoshifumi,Kitamata, Manabu,Matsuoka, Rei,Hanawa-Suetsugu, Kyoko,Senju, Yosuke,Mori, Masayuki X.,Kiyonaka, Shigeki,Kohda, Daisuke,Kitao, Akio,Mori, Yasuo,Suetsugu, Shiro,Akio Kitao","TRPV4 channel activity is modulated by direct interaction of the ankyrin domain to PI(4,5)P-2",,"Nature Communications",,"Vol. 5",,,2014,
"Yang, Lee-Wei,Kitao, Akio,Huang, Bang-Chieh,Go, Nobuhiro,Akio Kitao","Ligand-Induced Protein Responses and Mechanical Signal Propagation Described by Linear Response Theories",,"Biophysical Journal",,"Vol. 107","No. 6","pp. 1415-1425",2014,
"Omori, S.,Kitao, A.,Akio Kitao","CyClus: A fast, comprehensive cylindrical interface approximation clustering/reranking method for rigid-body proteinprotein docking decoys",,"Proteins-Structure Function and Bioinformatics",,"Vol. 81","No. 6","pp. 1005-1016",2013,
"Meshcheryakov, Vladimir A.,Kitao, Akio,Matsunami, Hideyuki,Samatey, Fadel A.,Akio Kitao","Inhibition of a type III secretion system by the deletion of a short loop in one of its membrane proteins",,"Acta Crystallographica Section D-Biological Crystallography",,"Vol. 69",,"pp. 812-820",2013,
"Ishikawa, Takeshi,Burri, Raghunadha Reddy,Kamatari, Yuji O.,Sakuraba, Shun,Matubayasi, Nobuyuki,Kitao, Akio,Kuwata, Kazuo,Akio Kitao","A theoretical study of the two binding modes between lysozyme and tri-NAG with an explicit solvent model based on the fragment molecular orbital method",,"Physical Chemistry Chemical Physics",,"Vol. 15","No. 10","pp. 3646-3654",2013,
"Yamamori, Yu,Kitao, Akio,Akio Kitao","MuSTAR MD: Multi-scale sampling using temperature accelerated and replica exchange molecular dynamics",,"Journal of Chemical Physics",,"Vol. 139","No. 14",,2013,
"Harada, Ryuhei,Kitao, Akio,Akio Kitao","Parallel cascade selection molecular dynamics (PaCS-MD) to generate conformational transition pathway",,"Journal of Chemical Physics",,"Vol. 139","No. 3",,2013,
"Takemura K,Guo H,Sakuraba S,Matubayasi N,Kitao A","Evaluation of protein-protein docking model structures using all-atom molecular dynamics simulations combined with the solution theory in the energy representation.",,,,,,,2012,Dec.
"Akio Kitao","The fast-folding mechanism of villin headpiece subdomain studied by multiscale distributed computing",,"Journal of Chemical Theory and Computation",,"Vol. 8","No. 1","pp. 290-299",2012,
"Akio Kitao","Water model tuning for improved reproduction of rotational diffusion and NMR spectral density",,"Journal of Physical Chemistry B",,"Vol. 116","No. 22","pp. 6279-6287",2012,
"Akio Kitao","Enhanced resolution of molecular recognition to distinguish structurally similar molecules by different conformational responses of a protein upon ligand binding",,"Journal of Structural Biology",,"Vol. 173","No. 1","pp. 20-28",2011,
"Akio Kitao","Transform and relax sampling for highly anisotropic systems: Application to protein domain motion and folding",,"Journal of Chemical Physics",,"Vol. 135","No. 4",,2011,
"Akio Kitao","Screw motion regulates multiple functions of T4 phage protein gene product 5 during cell puncturing",,"Journal of the American Chemical Society",,"Vol. 133","No. 34","pp. 13571-13576",2011,
"Akio Kitao","Multi-Scale Free Energy Landscape calculation method by combination of coarse-grained and all-atom models",,"Chemical Physics Letters",,"Vol. 503","No. 1-3","pp. 145-152",2011,
"Akio Kitao","Exploring the folding free energy landscape of a β-hairpin miniprotein, chignolin, using multiscale free energy landscape calculation method",,"Journal of Physical Chemistry B",,"Vol. 115","No. 27","pp. 8806-8812",2011,
"Akio Kitao","Erratum: Transform and relax sampling for highly anisotropic systems: Application to protein domain motion and folding (Journal of Chemical Physics (2011) 135 (045101))",,"Journal of Chemical Physics",,"Vol. 135","No. 11",,2011,
"Akio Kitao","Erratum: Multi-Scale Free Energy Landscape calculation method by combination of coarse-grained and all-atom models (Chemical Physics Letters (2011) 503 (145-152))",,"Chemical Physics Letters",,"Vol. 516","No. 1-3",,2011,
"Akio Kitao","Mechanical unfolding of bacterial flagellar filament protein by molecular dynamics simulation",,"Journal of Molecular Graphics and Modelling",,"Vol. 28","No. 6","pp. 548-554",2010,
"Akio Kitao","The effect of end constraints on protein loop kinematics",,"Biophysical Journal",,"Vol. 98","No. 9","pp. 1976-1985",2010,
"Akio Kitao","Structure of the cytoplasmic domain of FlhA and implication for flagellar type III protein export",,"Molecular Microbiology",,"Vol. 76","No. 1","pp. 260-268",2010,
"Akio Kitao","Detecting coupled collective motions in protein by independent subspace analysis",,"Journal of Chemical Physics",,"Vol. 133","No. 18",,2010,
"Akio Kitao","Collective dynamics of periplasmic glutamine binding protein upon domain closure",,"Biophysical Journal",,"Vol. 97","No. 9","pp. 2541-2549",2009,
"Akio Kitao","Principal component analysis of native ensembles of biomolecular structures (PCA_NEST): Insights into functional dynamics",,"Bioinformatics",,"Vol. 25","No. 5","pp. 606-614",2009,
"Akio Kitao","Multiple Markov transition matrix method: Obtaining the stationary probability distribution from multiple simulations",,"Journal of Computational Chemistry",,"Vol. 30","No. 12","pp. 1850-1858",2009,
"Akio Kitao","Erratum: Principal component analysis of native ensembles of biomolecular structures (PCA_NEST): Insights into functional dynamics (Bioinformatics (2009) vol. 25 (5) (606-614))",,"Bioinformatics",,"Vol. 25","No. 16",,2009,
"Akio Kitao","DTA: Dihedral transition analysis for characterization of the effects of large main-chain dihedral changes in proteins",,"Bioinformatics",,"Vol. 25","No. 5","pp. 628-635",2009,
"Akio Kitao","Hydration effect on low-frequency protein dynamics observed in simulated neutron scattering spectra",,"Biophysical Journal",,"Vol. 94","No. 11","pp. 4435-4443",2008,
"Akio Kitao","Hydration affects both harmonic and anharmonic nature of protein dynamics",,"Biophysical Journal",,"Vol. 95","No. 6","pp. 2916-2923",2008,
"Akio Kitao","Thermal unfolding simulations of bacterial flagellin: Insight into its refolding before assembly",,"Biophysical Journal",,"Vol. 94","No. 10","pp. 3858-3871",2008,
"Akio Kitao","Hydration-dependent protein dynamics revealed by molecular dynamics simulation of crystalline staphylococcal nuclease",,"Journal of Physical Chemistry B",,"Vol. 112","No. 11","pp. 3522-3528",2008,
"Tadaomi Furuta,Fadel A. Samatey,Hideyuki Matsunami,Katsumi Imada,Keiichi Namba,Akio Kitao","Gap compression/extension mechanism of bacterial flagellar hook as the molecular universal joint",,"J. Struct. Biol.",,"Vol. 157","No. 3","pp. 481-490",2007,Mar.
"Akio Kitao","Non-Gaussian behavior of elastic incoherent neutron scattering profiles of proteins studied by molecular dynamics simulation",,"Physical Review E - Statistical, Nonlinear, and Soft Matter Physics",,"Vol. 75","No. 4",,2007,
"Akio Kitao","Effects of water model and simulation box size on protein diffusions motions",,"Journal of Physical Chemistry B",,"Vol. 111","No. 41","pp. 11870-11872",2007,
"Akio Kitao","Picosecond fluctuating protein energy landscape mapped by pressure-temperature molecular dynamics simulation",,"Proceedings of the National Academy of Sciences of the United States of America",,"Vol. 104","No. 44","pp. 17261-17265",2007,
"Akio Kitao","Amplitudes and directions of internal protein motions from a JAM analysis of 15N relaxation data",,"Magnetic Resonance in Chemistry",,"Vol. 44","No. 7 SPEC. ISS.",,2006,
"Akio Kitao","Protein energy landscape and dynamics studied by molecular simulations and neutron scattering",,"Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme.",,"Vol. 51","No. 8","pp. 972-978",2006,
"Akio Kitao","Switch interactions control energy frustration and multiple flagellar filament structures",,"Proceedings of the National Academy of Sciences of the United States of America",,"Vol. 103","No. 13","pp. 4894-4899",2006,
"Akio Kitao","Molecular dynamics simulations of NAD+-induced domain closure in horse liver alcohol dehydrogenase",,"Biophysical Journal",,"Vol. 91","No. 5","pp. 1823-1831",2006,
"Akio Kitao","Hydration-coupled protein boson peak measured by incoherent neutron scattering",,"Physica B: Condensed Matter",,"Vol. 385-386",,"pp. 871-873",2006,
"Akio Kitao","Dynamical heterogeneity of protein dynamics studied by elastic incoherent neutron scattering and molecular simulations",,"Materials Science and Engineering A",,"Vol. 442","No. 1-2 SPEC. ISS.","pp. 356-360",2006,
"Akio Kitao","Universal joint of biological supramolecule: mechanism of bacterial flagellar hook investigated in silico",,"Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme",,"Vol. 50","No. 10 Suppl","pp. 1335-1340",2005,
"Akio Kitao","Structure, function and self-assembly of the bacterial flagellum",,"Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme",,"Vol. 50","No. 10 Suppl","pp. 1328-1334",2005,
"Akio Kitao","Protein boson peak originated from hydration-related multiple minima energy landscape",,"Journal of the American Chemical Society",,"Vol. 127","No. 24","pp. 8705-8709",2005,
"Akio Kitao","Structure of the bacterial flagellar hook and implication for the molecular universal joint mechanism",,"Nature",,"Vol. 431","No. 7012","pp. 1062-1068",2004,
"Akio Kitao","Molecular simulation study to examine the possibility of detecting collective motion in protein by inelastic neutron scattering",,"Physica B: Condensed Matter",,"Vol. 350","No. 1-3 SUPPL. 1",,2004,
"Akio Kitao","How can free energy component analysis explain the difference in protein stability caused by amino acid substitutions? Effect of three hydrophobic mutations at the 56th residue on the stability of human lysozyme",,"Protein Engineering",,"Vol. 16","No. 9","pp. 665-671",2003,
"Akio Kitao","The Effects of Solvent and Anharmonicity on Incoherent Inelastic Neutron Scattering Spectra of Proteins",,,,,,,2002,Jan.
"Akio Kitao","Multidimensional replica-exchange method for free-energy calculations",,,,,,,2000,
"Akio Kitao","A Novel Method to Investigate Functionally-relevant Protein Dynamics.",,,,,,,2000,
"Akio Kitao","A space-time structure determination of human CD2 reveals the CD58-binding mode",,"Proceedings of the National Academy of Sciences of the United States of America",,"Vol. 97","No. 5","pp. 2064-2068",2000,
"Akio Kitao","Molecular dynamics simulation shows large volume fluctuations of proteins",,"European Biophysics Journal",,"Vol. 29","No. 7","pp. 472-480",2000,
"Akio Kitao","Investigating protein dynamics in collective coordinate space",,"Current Opinion in Structural Biology",,"Vol. 9","No. 2","pp. 164-169",1999,
"Akio Kitao","Computational analysis of thermal stability: effect of Ile→Val mutations in human lysozyme",,,,,,,1998,June
"Akio Kitao","Dependence of protein stability on the structure of the denatured state: Free energy calculations of 156V mutation in human lysozyme",,"Biophysical Journal",,"Vol. 75","No. 5","pp. 2178-2187",1998,
"Akio Kitao","Protein electron transfer reorganization energy spectrum from normal mode analysis. 2. Application to ru-modified cytochrome c",,"Journal of Physical Chemistry B",,"Vol. 102","No. 11","pp. 2085-2094",1998,
"Akio Kitao","Protein electron transfer reorganization energy spectrum from normal mode analysis. 1. Theory",,"Journal of Physical Chemistry B",,"Vol. 102","No. 11","pp. 2076-2084",1998,
"Akio Kitao","Improved protein free energy calculation by more accurate treatment of nonbonded energy: Application to chymotrypsin inhibitor 2, V57A",,"Proteins: Structure, Function and Genetics",,"Vol. 30","No. 4","pp. 388-400",1998,
"Akio Kitao","Energy landscape of a native protein: Jumping-among-minima model",,"Proteins: Structure, Function and Genetics",,"Vol. 33","No. 4","pp. 496-517",1998,
"Akio Kitao","Model-free methods of analyzing domain motions in proteins from simulation: A comparison of normal mode analysis and molecular dynamics simulation of lysozyme",,"Proteins: Structure, Function and Genetics",,"Vol. 27","No. 3","pp. 425-437",1997,
"Akio Kitao","Harmonicity and anharmonicity in protein dynamics: A normal mode analysis and principal component analysis",,"Proteins: Structure, Function and Genetics",,"Vol. 23","No. 2","pp. 177-186",1995,
"Akio Kitao","Harmonic and anharmonic aspects in the dynamics of BPTI: A normal mode analysis and principal component analysis",,"Protein Science",,"Vol. 3","No. 6","pp. 936-943",1994,
"Akio Kitao","A collective motion description of the 310-/α-helix transition: Implications for a natural reaction coordinate",,"Journal of the American Chemical Society",,"Vol. 116","No. 14","pp. 6307-6315",1994,
"Akio Kitao","Comparison of normal mode analyses on a small globular protein in dihedral angle space and Cartesian coordinate space",,"Biophysical Chemistry",,"Vol. 52","No. 2","pp. 107-114",1994,
"Akio Kitao","Effects of solvent on the conformation and the collective motions of a protein. 2. Structure of hydration in melittin",,"Journal of Physical Chemistry",,"Vol. 97","No. 39","pp. 10223-10230",1993,
"Akio Kitao","Effects of solvent on the conformation and the collective motions of a protein. 3. Free energy analysis by the extended RISM theory",,"Journal of Physical Chemistry",,"Vol. 97","No. 39","pp. 10231-10235",1993,
"Akio Kitao","Effect of solvent on collective motions in globular protein",,"Journal of Molecular Biology",,"Vol. 234","No. 4","pp. 1207-1217",1993,
"Akio Kitao","The effects of solvent on the conformation and the collective motions of protein: Normal mode analysis and molecular dynamics simulations of melittin in water and in vacuum",,"Chemical Physics",,"Vol. 158","No. 2-3","pp. 447-472",1991,
"Kitao, A.,Go, N.,Akio Kitao","CONFORMATIONAL DYNAMICS OF POLYPEPTIDES AND PROTEINS IN THE DIHEDRAL ANGLE SPACE AND IN THE CARTESIAN COORDINATE SPACE - NORMAL MODE ANALYSIS OF DECA-ALANINE",,"Journal of Computational Chemistry",,"Vol. 12","No. 3","pp. 359-368",1991,