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Softness-function relationship in large molecules and molecular assemblies investigated at atomic resolution

Planned Research

Project AreaScience on Function of Soft Molecular Systems by Cooperation of Theory and Experiment
Project/Area Number 25104002
Research Category

Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)

Allocation TypeSingle-year Grants
Review Section Science and Engineering
Research InstitutionTokyo Institute of Technology (2017)
The University of Tokyo (2013-2016)

Principal Investigator

KITAO Akio  東京工業大学, 生命理工学院, 教授 (30252422)

Project Period (FY) 2013-06-28 – 2018-03-31
Project Status Completed (Fiscal Year 2017)
Budget Amount *help
¥119,210,000 (Direct Cost: ¥91,700,000、Indirect Cost: ¥27,510,000)
Fiscal Year 2017: ¥22,750,000 (Direct Cost: ¥17,500,000、Indirect Cost: ¥5,250,000)
Fiscal Year 2016: ¥22,880,000 (Direct Cost: ¥17,600,000、Indirect Cost: ¥5,280,000)
Fiscal Year 2015: ¥22,750,000 (Direct Cost: ¥17,500,000、Indirect Cost: ¥5,250,000)
Fiscal Year 2014: ¥22,880,000 (Direct Cost: ¥17,600,000、Indirect Cost: ¥5,280,000)
Fiscal Year 2013: ¥27,950,000 (Direct Cost: ¥21,500,000、Indirect Cost: ¥6,450,000)
Keywords柔らかさ / ダイナミクス / 巨大分子 / 分子集合体 / 機能 / ダイナイミクス
Outline of Final Research Achievements

We have investigated softness of complex molecular systems by developing simulation methods, and applying them to investigate softness-function relationship. To investigate relationship between softness and function, we developed simulation methods, MuSTAR MD and PaCS-MD, by considering features of soft molecular systems. In collaboration with the researchers in A02, we carefully compared computational and theoretical results as seen in the study of DNA and RNA hairpin structure formation and stability. In collaboration with the researchers in A03, we predicted and designed protein structure and function as seen in the case of DNA photolyase studies.

Report

(6 results)
  • 2017 Annual Research Report   Final Research Report ( PDF )
  • 2016 Annual Research Report
  • 2015 Annual Research Report
  • 2014 Annual Research Report
  • 2013 Annual Research Report
  • Research Products

    (76 results)

All 2018 2017 2016 2015 2014 2013 Other

All Int'l Joint Research (3 results) Journal Article (29 results) (of which Int'l Joint Research: 8 results,  Peer Reviewed: 28 results,  Open Access: 15 results,  Acknowledgement Compliant: 10 results) Presentation (38 results) (of which Int'l Joint Research: 10 results,  Invited: 26 results) Book (1 results) Remarks (5 results)

  • [Int'l Joint Research] University of East Anglia(英国)

    • Related Report
      2017 Annual Research Report
  • [Int'l Joint Research] 国立精華大学(台湾)

    • Related Report
      2017 Annual Research Report
  • [Int'l Joint Research] University of East Anglia(英国)

    • Related Report
      2015 Annual Research Report
  • [Journal Article] Multi-strand β-sheet of Alzheimer Aβ(1-40) folds to β-strip helix: Implication for protofilament formation2018

    • Author(s)
      Steven Hayward, Akio Kitao
    • Journal Title

      Journal of Biomolecular Structure and Dynamics

      Volume: 印刷中

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Molecular dynamics simulation of bacterial flagella2018

    • Author(s)
      Kitao Akio、Hata Hiroaki
    • Journal Title

      Biophysical Reviews

      Volume: 10 Issue: 2 Pages: 203-208

    • DOI

      10.1007/s12551-017-0338-7

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Binding free energy analysis of protein-protein docking model structures by evERdock2018

    • Author(s)
      Takemura Kazuhiro、Matubayasi Nobuyuki、Kitao Akio
    • Journal Title

      J. Chem. Phys.

      Volume: 148 Issue: 10 Pages: 105101-105101

    • DOI

      10.1063/1.5019864

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Origins of biological function in DNA and RNA hairpin loop motifs from replica exchange molecular dynamics simulation2018

    • Author(s)
      Jacob B. Swadling, Kunihiko Ishii, Tahei Tahara and Akio Kitao
    • Journal Title

      Physical Chemistry Chemical Physics

      Volume: 20 Issue: 5 Pages: 2990-3001

    • DOI

      10.1039/c7cp06355e

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Protein-Ligand Dissociation Simulated by Parallel Cascade Selection Molecular Dynamics2017

    • Author(s)
      Tran Duy Phuoc、Takemura Kazuhiro、Kuwata Kazuo、Kitao Akio
    • Journal Title

      Journal of Chemical Theory and Computation

      Volume: 14 Issue: 1 Pages: 404-417

    • DOI

      10.1021/acs.jctc.7b00504

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Salt Bridge Formation between the I-BAR Domain and Lipids Increases Lipid Density and Membrane Curvature.2017

    • Author(s)
      Takemura K, Hanawa-Suetsugu K, Suetsugu S, Kitao A.
    • Journal Title

      Sci Rep.

      Volume: 28 Issue: 1 Pages: 1-10

    • DOI

      10.1038/s41598-017-06334-5

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Electron Fate and Mutational Robustness in the Mechanism of (6-4)Photolyase-Mediated DNA Repair2017

    • Author(s)
      Dokainish Hisham M.、Yamada Daichi、Iwata Tatsuya、Kandori Hideki、Kitao Akio
    • Journal Title

      ACS Catalysis

      Volume: 7 Issue: 7 Pages: 4835-4845

    • DOI

      10.1021/acscatal.7b00751

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Structure of the MotA/B Proton Channel2017

    • Author(s)
      Kitao Akio、Nishihara Yasutaka
    • Journal Title

      Methods in molecular biology

      Volume: 1593 Pages: 133-145

    • DOI

      10.1007/978-1-4939-6927-2_10

    • ISBN
      9781493969265, 9781493969272
    • Related Report
      2017 Annual Research Report
    • Peer Reviewed
  • [Journal Article] High quality rendering of protein dynamics in space filling mode2017

    • Author(s)
      Matthews Nick、Easdon Robert、Kitao Akio、Hayward Steven、Laycock Stephen
    • Journal Title

      Journal of Molecular Graphics & Modellin

      Volume: 78 Pages: 158-167

    • DOI

      10.1016/j.jmgm.2017.09.017

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Molecular Dynamics Study of Nitrogen-Pyramidalized Bicyclic β-Proline Oligomers: Length-Dependent Convergence to Organized Structure2017

    • Author(s)
      Yuko Otani, Satoshi Watanabe, Tomohiko Ohwada, Akio Kitao
    • Journal Title

      The Journal of Physical Chemistry B

      Volume: 121 Issue: 1 Pages: 100-109

    • DOI

      10.1021/acs.jpcb.6b10668

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Functional Conversion of CPD and (6-4) Photolyases by Mutation2016

    • Author(s)
      Daichi Yamada, Hisham M. Dokainish, Tatsuya Iwata, Junpei Yamamoto, Tomoko Ishikawa, Takeshi Todo, Shigenori Iwai, Elizabeth D. Getzoff, Akio Kitao, and Hideki Kandori
    • Journal Title

      Biochemistry

      Volume: 55 Issue: 30 Pages: 4173-4183

    • DOI

      10.1021/acs.biochem.6b00361

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] Computational Assignment of the Histidine Protonation State in (6-4) Photolyase Enzyme and Its Effect on the Protonation Step2016

    • Author(s)
      Hisham MM Dokainish and Akio Kitao
    • Journal Title

      ACS Catalysis

      Volume: 6 Issue: 8 Pages: 5500-5507

    • DOI

      10.1021/acscatal.6b01094

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Parallel Cascade Selection Molecular Dynamics for Efficient Conformational Sampling and Free Energy Calculation of Proteins2016

    • Author(s)
      Akio Kitao, Tyuhei Harada, Yasutaka Nishihara and Duy Phuoc Tran
    • Journal Title

      AIP Conference Proceedings

      Volume: 1790 Pages: 020013-020013

    • DOI

      10.1063/1.4968639

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] High anisotropy and frustration: the keys to regulating protein function efficiently in crowded environments2016

    • Author(s)
      Akio Kitao and Kazuhiro Takemura
    • Journal Title

      Curr Opin Struct Biol

      Volume: 42 Pages: 50-58

    • DOI

      10.1016/j.sbi.2016.10.014

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Eritoran inhibits S100A8-mediated TLR4/MD-2 activation and tumor growth by changing the immune microenvironment.2016

    • Author(s)
      Deguchi A, Tomita T, Ohto U, Takemura K, Kitao A, Akashi-Takamura, S, Miyake K, and Maru Y.
    • Journal Title

      Oncogene

      Volume: 35 Issue: 11 Pages: 1445-1456

    • DOI

      10.1038/onc.2015.211

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] Gate-controlled proton diffusion and protonation-induced ratchet motion in the stator of the bacterial flagellar motor2015

    • Author(s)
      Yasutaka Nishihara and Akio Kitao
    • Journal Title

      Proc. Natl. Acad. Sci. U.S.A.

      Volume: 112 Issue: 25 Pages: 7737-7742

    • DOI

      10.1073/pnas.1502991112

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Drug Targeting Based on a New Concept-Targeting Against TLR4 as an Example2015

    • Author(s)
      Yoshiro Maru, Takeshi Tomita, Atsuko Deguchi, Katsuaki Ieguchi, Morichuka Takita, Fujiko Tsukahara, Kazuhiro Takemura, Akio Kitao, and Fabian Gusovsky
    • Journal Title

      Endocrine Metabolic & Immune Disorders-Drug Targets

      Volume: 15 Issue: 2 Pages: 83-87

    • DOI

      10.2174/187153031502150522123746

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Monte Carlo Sampling with Linear Inverse Kinematics for Simulation of Proteins Flexible Regions2015

    • Author(s)
      Steven Hayward and Akio Kitao
    • Journal Title

      J. Chem. Theor. Comput.

      Volume: 11 Issue: 8 Pages: 3895-3905

    • DOI

      10.1021/acs.jctc.5b00215

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] Non-targeted parallel cascade selection molecular dynamics (nt-PaCS-MD) for enhancement of the conformational sampling of proteins2015

    • Author(s)
      Ryuhei Harada and Akio Kitao
    • Journal Title

      J. Chem. Theor. Comput.

      Volume: 11 Issue: 11 Pages: 5493-5502

    • DOI

      10.1021/acs.jctc.5b00723

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Design, synthesis and structure-activity relationship studies of novel sirtuin 2 (SIRT2) inhibitors with a benzamide skeleton.2015

    • Author(s)
      Taki Sakai, Yotaro Matsumoto, Minoru Ishikawa, Kazuyuki Sugita, Yuichi Hashimoto, Nobuhiko Wakai, Akio Kitao, Era Morishita, Chikashi Toyoshima, Tomoatsu Hayashi, Tetsu Akiyama
    • Journal Title

      Bioorg Med Chem.

      Volume: 23 Issue: 2 Pages: 328-339

    • DOI

      10.1016/j.bmc.2014.11.027

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] TRPV4 channel activity is modulated by direct interaction of the ankyrin domain to PI(4,5)P22014

    • Author(s)
      Nobuaki Takahashi, Sayaka Hamada-Nakahara, Yuzuru Itoh, Kazuhiro Takemura, Atsushi Shimada,Yoshifumi Ueda, Manabu Kitamata, Rei Matsuoka, Kyoko Hanawa-Suetsugu, Yosuke Senju, Masayuki X. Mori, Shigeki Kiyonaka, Daisuke Kohda, Akio Kitao, Yasuo Mori and Shiro Suetsugu
    • Journal Title

      Nature Communications

      Volume: 5 Issue: 1 Pages: 4994-4994

    • DOI

      10.1038/ncomms5994

    • NAID

      130005100825

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Ligand-Induced Protein Responses and Mechanical Signal Propagation Described by Linear Response Theories2014

    • Author(s)
      Lee-Wei Yang, Akio Kitao, Bang-chieh Huang and Nobuhiro Go
    • Journal Title

      Biophysical Journal

      Volume: 107 Issue: 6 Pages: 1415-1425

    • DOI

      10.1016/j.bpj.2014.07.049

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Molecular Simulation Methods to Enhance Soft Protein Motions2014

    • Author(s)
      原田隆平,北尾彰朗
    • Journal Title

      Seibutsu Butsuri

      Volume: 54 Issue: 3 Pages: 167-171

    • DOI

      10.2142/biophys.54.167

    • NAID

      130004719369

    • ISSN
      0582-4052, 1347-4219
    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] カスケード型超並列シミュレーションによるタンパク質構造遷移のパスウェイ探索2014

    • Author(s)
      西原泰孝, 原田隆平, 北尾彰朗
    • Journal Title

      統計数理

      Volume: 62 Pages: 273-284

    • NAID

      120006020818

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Conformational transition pathway and free energy analyses of proteins by parallel cascade selection molecular dynamics (PaCS-MD)2014

    • Author(s)
      Ryuhei Harada, Yasutaka Nishihara, Nobuhiko Wakai, and Akio Kitao
    • Journal Title

      AIP Conference Proceedings

      Volume: 1618 Pages: 86-86

    • DOI

      10.1063/1.4897682

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Mechanism of Deep-sea Fish α-Actin Pressure Tolerance Investigated by Molecular Dynamics Simulations2014

    • Author(s)
      Nobuyuki Wakai and Akio Kitao
    • Journal Title

      PLoS ONE

      Volume: 9 Issue: 1 Pages: e85852-e85852

    • DOI

      10.1371/journal.pone.0085852

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Parallel cascade selection molecular dynamics (PaCS-MD) to generate conformational transition pathway2013

    • Author(s)
      Ryuhei Harada and Akio Kitao
    • Journal Title

      Journal of Chemical Physics

      Volume: 139 Issue: 3

    • DOI

      10.1063/1.4813023

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] MuSTAR MD: Multi-scale sampling using temperature accelerated and replica exchange molecular dynamics2013

    • Author(s)
      Yu Yamamori and Akio Kitao
    • Journal Title

      Journal of Chemical Physics

      Volume: 139 Issue: 14

    • DOI

      10.1063/1.4823743

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] 分子シミュレーションによるタンパク質ダイナミクスとテラヘルツ分光2013

    • Author(s)
      城地保昌,北尾彰朗
    • Journal Title

      化学工業

      Volume: 64 Pages: 7-13

    • Related Report
      2013 Annual Research Report
  • [Presentation] カスケード型超並列シミュレーションでみるCheY-FliM複合体解離に対する圧力の影響2018

    • Author(s)
      畑宏明、北尾彰朗
    • Organizer
      2017年度べん毛研究交流会
    • Related Report
      2017 Annual Research Report
  • [Presentation] Na+駆動型べん毛モーターPomA/PomBのThr残基のイオン透過における役割MDシミュレーション結果2018

    • Author(s)
      尾上靖宏, 岩城雅代,信夫愛、西原泰孝、岩月哲人、寺島浩行、北尾 彰朗、神取秀樹、本間道夫
    • Organizer
      2017年度べん毛研究交流会
    • Related Report
      2017 Annual Research Report
  • [Presentation] PaCS-MDによるタンパク質のダイナミクスと離合集散2018

    • Author(s)
      北尾彰朗
    • Organizer
      物性研究所スパコン共同利用・CCMS合同研究会「計算物質科学の今と未来」
    • Related Report
      2017 Annual Research Report
    • Invited
  • [Presentation] 分子シミュレーションによる細菌べん毛モーターの分子機構2017

    • Author(s)
      北尾彰朗
    • Organizer
      日本物理学会第72回年次大会
    • Place of Presentation
      大阪大学豊中キャンパス(大阪市豊中市)
    • Year and Date
      2017-03-17
    • Related Report
      2016 Annual Research Report
    • Invited
  • [Presentation] 実験と計算によるp53 の標的DNA 配列探索機能(1)2017

    • Author(s)
      北尾彰朗
    • Organizer
      日本化学会第97春季年会
    • Place of Presentation
      慶應義塾大学日吉キャンパス(神奈川県横浜市)
    • Year and Date
      2017-03-16
    • Related Report
      2016 Annual Research Report
    • Invited
  • [Presentation] Dynamic structure of bacterial flagellar proteins observed in silico2017

    • Author(s)
      Akio Kitao
    • Organizer
      Bacterial Flagella, Injectisome and Type III Secretion Systems
    • Place of Presentation
      沖縄科学技術大学院大学(沖縄県恩納村)
    • Year and Date
      2017-03-01
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research
  • [Presentation] PaCS-MDでみる蛋白質の柔らかさ・離合集散と機能2017

    • Author(s)
      北尾彰朗
    • Organizer
      第17回日本蛋白質科学会年会
    • Related Report
      2017 Annual Research Report
    • Invited
  • [Presentation] Electron fate and mutational robustness in the mechanism of (6-4) photolyase-mediated DNA repair2017

    • Author(s)
      Hisham M. Dokainish, Daichi Yamada, Tatsuya Iwata, Hideki Kandori and Akio Kitao
    • Organizer
      5th AWEST 2017 the 5th Awaji International Workshop on “Electron Spin Science & Technology: Biological and Materials Science Oriented Applications”
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Protein-protein complex structure prediction using the solution theory in the energy representation2017

    • Author(s)
      竹村和浩, 松林伸幸, 北尾彰朗
    • Organizer
      第55回日本生物物理学会
    • Related Report
      2017 Annual Research Report
  • [Presentation] MD シミュレーションを用いた構造サンプリングによるドッキングタンパク質ータンパク質複合体結合自由エネルギー評価の精密化2017

    • Author(s)
      信夫愛, 竹村和浩, 北尾彰朗
    • Organizer
      第55回日本生物物理学会
    • Related Report
      2017 Annual Research Report
  • [Presentation] Improvement of PaCS-MD based Flexible Docking Methods2017

    • Author(s)
      Phuoc Duy Tran and Akio Kitao
    • Organizer
      第55回日本生物物理学会
    • Related Report
      2017 Annual Research Report
  • [Presentation] 生体高分子の離合集散ダイナミクス2017

    • Author(s)
      北尾彰朗
    • Organizer
      第66回高分子討論会
    • Related Report
      2017 Annual Research Report
    • Invited
  • [Presentation] Electron fate and mutational robustness in the mechanism of (6-4) photolyase-mediated DNA repair2017

    • Author(s)
      Dokainish Hisham M.、Yamada Daichi、Iwata Tatsuya、Kandori Hideki、Kitao Akio
    • Organizer
      WATOC2017-World Association of Theoretical and Computational Chemists
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Refining binding free energies of docked complexes by sampling configurations during molecular dynamics simulations2017

    • Author(s)
      Ai Shinobu Kazuhiro Takemura Akio Kitao
    • Organizer
      Conformational Ensembles from Experimental Data and Computer Simulations
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Protein-peptide dissociation at high pressure studied by parallel cascade selection molecular dynamics simulations2017

    • Author(s)
      畑宏明, 西原泰孝, 西山雅祥, 川岸 郁朗, 北尾彰朗
    • Organizer
      第55回日本生物物理学会
    • Related Report
      2017 Annual Research Report
  • [Presentation] Refining binding free energies of docked protein-protein complexes by sampling conformations during molecular dynamics simulations2017

    • Author(s)
      Ai Shinobu Kazuhiro Takemura Akio Kitao
    • Organizer
      第56回日本生物物理学会
    • Related Report
      2017 Annual Research Report
  • [Presentation] Dissociation and Association Dynamics of Proteins2017

    • Author(s)
      Akio Kitao
    • Organizer
      TSCR Workshop on Protein Dynamics
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Simulating biomolecular interactions and functions2016

    • Author(s)
      Akio Kitao
    • Organizer
      1st International Symposium on Research and Education of Computational Science (RECS)
    • Place of Presentation
      東京大学小柴ホール(東京都文京区)
    • Year and Date
      2016-11-29
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] DNA光回復酵素の機能発現メカニズム2016

    • Author(s)
      北尾彰朗、神取秀樹
    • Organizer
      「柔らかな分子系」第4回公開シンポジウム
    • Place of Presentation
      名古屋工業大学(愛知県名古屋市)
    • Year and Date
      2016-10-27
    • Related Report
      2016 Annual Research Report
  • [Presentation] Parallel cascade selection molecular dynamics for efficient conformational sampling of biomolecular systems2016

    • Author(s)
      Akio Kitao
    • Organizer
      International Conference on Molecular Simulation 2016
    • Place of Presentation
      上海交通大学(中国上海市)
    • Year and Date
      2016-10-23
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] タンパク質との相互作用による脂質膜の構造変化ダイナミクス2016

    • Author(s)
      北尾彰朗
    • Organizer
      第89回日本生化学会大会
    • Place of Presentation
      仙台国際センター(宮城県仙台市)
    • Year and Date
      2016-09-25
    • Related Report
      2016 Annual Research Report
    • Invited
  • [Presentation] Structure, dynamics, and function of bacterial flagella investigated by molecular dynamics simulation2015

    • Author(s)
      Akio Kitao
    • Organizer
      The International Chemical Congress of Pacific Basin Societies 2015
    • Place of Presentation
      Honolulu, HI, USA
    • Year and Date
      2015-12-15
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Solvation effects on protein interaction with other molecules2015

    • Author(s)
      Akio Kitao
    • Organizer
      Symposium of 53rd Annual Meeting of the Biophysical Society of Japan
    • Place of Presentation
      金沢大学角間キャンパス(石川県・金沢市)
    • Year and Date
      2015-09-13
    • Related Report
      2015 Annual Research Report
    • Invited
  • [Presentation] Parallel Cascade Selection Molecular Dynamics (PaCS-MD) to explore conformational spaces of proteins efficiently2015

    • Author(s)
      Akio Kitao
    • Organizer
      Workshop on Kinetics of Enzymes and Molecular Machines
    • Place of Presentation
      Beijing, China
    • Year and Date
      2015-08-18
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Proton permeation mechanisms in the stator of bacterial flagellar motor2015

    • Author(s)
      Akio Kitao
    • Organizer
      Telluride Research Center Workshop on Protein Dynamics
    • Place of Presentation
      Telluride, CO, USA
    • Year and Date
      2015-08-03
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Dynamics and Function of Bacterial Flagella Investigated by Molecular Simulation2015

    • Author(s)
      Akio Kitao
    • Organizer
      The 20th Biophysics Conference
    • Place of Presentation
      Academia Sinica, 台北、台湾
    • Year and Date
      2015-05-12
    • Related Report
      2015 Annual Research Report
    • Invited
  • [Presentation] Membrane deformation induced by proteins2015

    • Author(s)
      Akio Kitao
    • Organizer
      分子研研究会「生体分子の構造、ダイナッミクス、機能」「Architecture, dynamics, and functionality of molecular biosystems」
    • Place of Presentation
      自然科学研究機構 分子研 研究棟201セミナー室(愛知県・岡崎市)
    • Year and Date
      2015-03-30 – 2015-03-31
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] 高度な分子動力学によるタンパク質の機能シミュレーション2015

    • Author(s)
      北尾彰朗
    • Organizer
      スーパーコンピュータワークショップ2015
    • Place of Presentation
      岡崎コンファレンスセンター(愛知県・岡崎市)
    • Year and Date
      2015-01-29 – 2015-01-30
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] Observing soft functional motion of proteins in silico2014

    • Author(s)
      Akio Kitao
    • Organizer
      第52回日本生物物理学会年会シンポジウム
    • Place of Presentation
      札幌コンベンションセンター(北海道・札幌市)
    • Year and Date
      2014-09-25 – 2014-09-27
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] Molecular simulation of proteins: Pressure tolerance of deep-sea fish actin and membrane deformation induced by I-BAR domain2014

    • Author(s)
      Akio Kitao
    • Organizer
      1st SPIRITS Workshop“Manipulation of Integrated Molecular Reaction Processes in living cell
    • Place of Presentation
      Kyoto/Campus Plaza Kyoto
    • Year and Date
      2014-09-02
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] Conformational Transition Pathway and Free Energy Analyses of Proteins by Parallel Cascade Selection Molecular Dynamics (PaCS-MD)2014

    • Author(s)
      Ryuhei Harada, Yasutaka Nishihara, Nobuhiko Wakai and Akio Kitao
    • Organizer
      International Conference of Computational Methods in Sciences and Engineering (ICCMSE 2014)
    • Place of Presentation
      Athens, Greece/Metropolitan Hotel
    • Year and Date
      2014-04-04 – 2014-04-07
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] バイオ分子が働く様子をコンピュータでみてみよう2014

    • Author(s)
      北尾彰朗
    • Organizer
      化学への招待-講演会;コンピュータ化学で物質の振舞いや生命現象を「見る」
    • Place of Presentation
      東京都目黒区/東大生産技術研究所コンベンションホール
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] 柔らかさを利用したタンパク質とその集合体の機能制御2014

    • Author(s)
      北尾彰朗
    • Organizer
      日本化学会 第94春季年会 シンポジウム
    • Place of Presentation
      愛知県名古屋市/名古屋大学東山キャンパス
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] How Can Soft Molecular Machinery Be Well-Regulated? Structure and Function of Bacterial Flagella2013

    • Author(s)
      Akio Kitao
    • Organizer
      第15回日韓分子科学シンポジウム
    • Place of Presentation
      兵庫県神戸市/ホテル北野プラザ六甲荘
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] 分子シミュレーションによる大腸菌べん毛モーター固定子MotA/Bの立体構造モデリングとプロトン透過メカニズム2013

    • Author(s)
      北尾彰朗
    • Organizer
      第3回分子モーター討論会
    • Place of Presentation
      東京都文京区/東京大学フードサイエンス棟中島董一郎記念ホール
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] Exploring protein conformational transition pathways with efficient molecular simulation method2013

    • Author(s)
      Akio Kitao
    • Organizer
      Telluride Science Research Center Protein Dynamics Workshop on Protein Dynamics
    • Place of Presentation
      Telluride, CO, USA
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] 集団座標による分子シミュレーションの解析2013

    • Author(s)
      北尾彰朗
    • Organizer
      第7回分子シミュレーションスクール」「TCCIウィンターカレッジ」
    • Place of Presentation
      愛知県岡崎市/岡崎コンファレンスセンター
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] 巨大生体超分子の構造転移制御メカニズム2013

    • Author(s)
      北尾彰朗
    • Organizer
      HPCI戦略プログラム 分野1×分野2 シンポジウムin 名大「生体分子複合システムを計算する-相互作用は何をもたらすのか-」
    • Place of Presentation
      愛知県名古屋市/名古屋大学IB電子情報館
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Book] In Silico創薬におけるスクリーニングの高速化、高精度化技術2018

    • Author(s)
      北尾彰朗、畑宏明(第2章第2節著)
    • Total Pages
      540
    • Publisher
      技術情報協会
    • ISBN
      9784861046889
    • Related Report
      2017 Annual Research Report
  • [Remarks] 北尾研究室

    • URL

      http://www.kitao.bio.titech.ac.jp/

    • Related Report
      2017 Annual Research Report
  • [Remarks] 北尾研究室 Web Service and Software Download

    • URL

      http://kitao02.bio.titech.ac.jp/

    • Related Report
      2017 Annual Research Report
  • [Remarks] Laboratory of Computational Protein Science

    • URL

      http://www.iam.u-tokyo.ac.jp/MolDes/

    • Related Report
      2015 Annual Research Report
  • [Remarks] 生理的に重要なイオンを運ぶ通り道TRPV4の新たな制御機構を解明

    • URL

      http://www.u-tokyo.ac.jp/public/public01_260926_02_j.html

    • Related Report
      2014 Annual Research Report
  • [Remarks] 東京大学分子細胞生物学研究所計算分子機能研究分野

    • URL

      http://www.iam.u-tokyo.ac.jp/MolDes/

    • Related Report
      2013 Annual Research Report

URL: 

Published: 2013-07-10   Modified: 2022-05-13  

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