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Tama Florence  TAMA FLORENCE

… Alternative Names

TAMA FLORENCE  タマ フロハンス

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Researcher Number 20648191
Other IDs
  • ORCIDhttps://orcid.org/0000-0003-2021-5618
Affiliation (Current) 2025: 名古屋大学, 理学研究科, 教授
2025: 国立研究開発法人理化学研究所, 計算科学研究センター, チームプリンシパル
Affiliation (based on the past Project Information) *help 2024: 名古屋大学, 理学研究科, 教授
2016 – 2019: 名古屋大学, 理学研究科, 教授
2015: 名古屋大学, 理学(系)研究科(研究院), 教授
2014: 独立行政法人理化学研究所, 計算科学研究機構, 研究ユニットリーダー
Review Section/Research Field
Principal Investigator
Transformative Research Areas, Section (II) / Biophysics / Structural biochemistry
Except Principal Investigator
Complex systems
Keywords
Principal Investigator
MD simulations / integrative modeling / intrinsically disordered / protein dynamics / striga / single-particle / database / molecular shapes / single molecules / 3D structure … More / dynamics / structure / Biomolecules / Cryo-EM / XFEL / 2D images … More
Except Principal Investigator
海外共同研究者受入 / 海外研究者招聘 / 海外講演者招聘 / 海外研究者受入 / 海外派遣 / 国際共同研究 / 電子顕微鏡 / 分子動力学法 / シミュレーション / 膜蛋白質 / 構造解析法 / 生体超分子複合体 / マルチスケール法 / 粗視化分子モデル / 膜タンパク質 / マルチスケール・マルチレゾリューション / フレキシブルフィッティグ / 一分子構造解析 / クライオ電子顕微鏡 / 分子動力学 Less
  • Research Projects

    (5 results)
  • Research Products

    (40 results)
  • Co-Researchers

    (12 People)
  •  Integrating data and simulation for dynamic structural biologyPrincipal Investigator

    • Principal Investigator
      TAMA FLORENCE
    • Project Period (FY)
      2024 – 2028
    • Research Category
      Grant-in-Aid for Transformative Research Areas (A)
    • Review Section
      Transformative Research Areas, Section (II)
    • Research Institution
      Nagoya University
  •  Database of Molecular Shapes and Diffraction Patterns for X-ray Free Electron Laser Data AnalysisPrincipal Investigator

    • Principal Investigator
      Tama Florence
    • Project Period (FY)
      2017 – 2019
    • Research Category
      Grant-in-Aid for Scientific Research (C)
    • Research Field
      Structural biochemistry
    • Research Institution
      Nagoya University
  •  コンピューティングを活用した寄生植物ストライガを抑制する生命機能分子の探索Principal Investigator

    • Principal Investigator
      TAMA FLORENCE
    • Project Period (FY)
      2017
    • Research Category
      Grant-in-Aid for JSPS Fellows
    • Research Field
      Biophysics
    • Research Institution
      Nagoya University
  •  Support activities aimed at international network formation in the research area of dynamic structural life sciences

    • Principal Investigator
      Kohda Daisuke
    • Project Period (FY)
      2015 – 2018
    • Research Category
      Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)
    • Review Section
      Complex systems
    • Research Institution
      Kyushu University
  •  Molecular dynamics simulations of protein complexes based on multi-resolution models

    • Principal Investigator
      Sugita Yuji
    • Project Period (FY)
      2014 – 2018
    • Research Category
      Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)
    • Review Section
      Complex systems
    • Research Institution
      Institute of Physical and Chemical Research

All 2020 2019 2018 2017 2016 2015 2014 Other

All Journal Article Presentation Book

  • [Book] Hybrid Methods for Macromolecular Modeling by Molecular Mechanics Simulations with Experimental Data. In: Nakamura H., Kleywegt G., Burley S., Markley J. (eds) Integrative Structural Biology with Hybrid Methods. Advances in Experimental Medicine and Biology, vol 11052018

    • Author(s)
      O Miyashita, F. Tama
    • Total Pages
      19
    • Publisher
      Springer, Singapore
    • ISBN
      9789811321993
    • Data Source
      KAKENHI-PROJECT-17K07305
  • [Journal Article] Reconstruction of low-resolution molecular structures from simulated atomic force microscopy images2020

    • Author(s)
      Dasgupta Bhaskar、Miyashita Osamu、Tama Florence
    • Journal Title

      Biochimica et Biophysica Acta (BBA) - General Subjects

      Volume: 1864 Issue: 2 Pages: 129420-129420

    • DOI

      10.1016/j.bbagen.2019.129420

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-16K07286, KAKENHI-PROJECT-17K07305
  • [Journal Article] Computational Protocol for Assessing the Optimal Pixel Size to Improve the Accuracy of Single-particle Cryo-electron Microscopy Maps2020

    • Author(s)
      Tiwari Sandhya P.、Chhabra Sahil、Tama Florence、Miyashita Osamu
    • Journal Title

      Journal of Chemical Information and Modeling

      Volume: - Issue: 5 Pages: 2570-2580

    • DOI

      10.1021/acs.jcim.9b01107

    • Peer Reviewed / Int'l Joint Research
    • Data Source
      KAKENHI-PROJECT-16K07286, KAKENHI-PROJECT-17K07305
  • [Journal Article] Integrative/Hybrid Modeling Approaches for Studying Biomolecules2020

    • Author(s)
      Srivastava Ashutosh、Tiwari Sandhya Premnath、Miyashita Osamu、Tama Florence
    • Journal Title

      Journal of Molecular Biology

      Volume: 432 Issue: 9 Pages: 2846-2860

    • DOI

      10.1016/j.jmb.2020.01.039

    • Peer Reviewed / Open Access
    • Data Source
      KAKENHI-PLANNED-19H05781, KAKENHI-PROJECT-16K07286, KAKENHI-PROJECT-17K07305, KAKENHI-PLANNED-20H05453
  • [Journal Article] Cryo-Cooling Effect on DHFR Crystal Studied by Replica-Exchange Molecular Dynamics Simulations2019

    • Author(s)
      Nagai Tetsuro、Tama Florence、Miyashita Osamu
    • Journal Title

      Biophysical Journal

      Volume: 116 Issue: 3 Pages: 395-405

    • DOI

      10.1016/j.bpj.2018.11.3139

    • Peer Reviewed
    • Data Source
      KAKENHI-PLANNED-26119006
  • [Journal Article] Acceleration of cryo-EM Flexible Fitting for Large Biomolecular Systems by Efficient Space Partitioning2019

    • Author(s)
      Mori Takaharu、Kulik Marta、Miyashita Osamu、Jung Jaewoon、Tama Florence、Sugita Yuji
    • Journal Title

      Structure

      Volume: 27 Issue: 1 Pages: 161-174.e3

    • DOI

      10.1016/j.str.2018.09.004

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-16K07286, KAKENHI-PROJECT-17K07305, KAKENHI-PLANNED-26119006
  • [Journal Article] Conformational dynamics of human protein kinase CK2α and its effect on function and inhibition2018

    • Author(s)
      Ashutosh Srivastava, Tsuyoshi Hirota, Stephan Irle and Florence Tama
    • Journal Title

      Proteins Structure Function and Genetics

      Volume: 86 Issue: 3 Pages: 344-353

    • DOI

      10.1002/prot.25444

    • NAID

      120006477488

    • Peer Reviewed / Int'l Joint Research
    • Data Source
      KAKENHI-PROJECT-17K07305, KAKENHI-PLANNED-26119006, KAKENHI-PROJECT-15H05590
  • [Journal Article] Role of Computational Methods in Going beyond X-ray Crystallography to Explore Protein Structure and Dynamics2018

    • Author(s)
      Srivastava Ashutosh、Nagai Tetsuro、Srivastava Arpita、Miyashita Osamu、Tama Florence
    • Journal Title

      International Journal of Molecular Sciences

      Volume: 19 Issue: 11 Pages: 3401-3401

    • DOI

      10.3390/ijms19113401

    • Peer Reviewed / Open Access
    • Data Source
      KAKENHI-PROJECT-16K07286, KAKENHI-PROJECT-17K07305, KAKENHI-PLANNED-26119006
  • [Journal Article] 1.Single-particle XFEL 3D reconstruction of ribosome-size particles based on Fourier slice matching: requirements to reach subnanometer resolution2018

    • Author(s)
      Nakano, M., Miyashita, O., Jonic, S., Tokuhisa, A. & Tama, F.
    • Journal Title

      J. Synchrotron Rad.

      Volume: 25 Issue: 4 Pages: 1010-1021

    • DOI

      10.1107/s1600577518005568

    • Peer Reviewed / Int'l Joint Research
    • Data Source
      KAKENHI-PROJECT-16K07286, KAKENHI-PROJECT-17K07305
  • [Journal Article] Gaussian mixture model for coarse-grained modeling from XFEL2018

    • Author(s)
      Nagai Tetsuro、Mochizuki Yuki、Joti Yasumasa、Tama Florence、Miyashita Osamu
    • Journal Title

      Optics Express

      Volume: 26 Issue: 20 Pages: 26734-26734

    • DOI

      10.1364/oe.26.026734

    • Peer Reviewed / Open Access
    • Data Source
      KAKENHI-PROJECT-16K07286, KAKENHI-PROJECT-17K07305, KAKENHI-PROJECT-16K05527
  • [Journal Article] Computational investigation of the conformational dynamics in Tom20-mitochondrial presequence tethered complexes2018

    • Author(s)
      Srivastava Arpita、Tama Florence、Kohda Daisuke、Miyashita Osamu
    • Journal Title

      Proteins: Structure, Function, and Bioinformatics

      Volume: 87 Issue: 1 Pages: 81-90

    • DOI

      10.1002/prot.25625

    • Peer Reviewed / Int'l Joint Research
    • Data Source
      KAKENHI-PLANNED-26119002, KAKENHI-PLANNED-26119006
  • [Journal Article] Searching for 3D structural models from a library of biological shapes using a few 2D experimental images2018

    • Author(s)
      Tiwari Sandhya P.、Tama Florence、Miyashita Osamu
    • Journal Title

      BMC Bioinformatics

      Volume: 19 Issue: 1 Pages: 320-320

    • DOI

      10.1186/s12859-018-2358-0

    • Peer Reviewed / Open Access
    • Data Source
      KAKENHI-PROJECT-16K07286, KAKENHI-PROJECT-17K07305
  • [Journal Article] Flexible fitting to cryo-EM density map using ensemble molecular dynamics simulations2017

    • Author(s)
      Miyashita O, Kobayashi C, Mori T, Sugita Y, Tama F
    • Journal Title

      J. Comp. Chem

      Volume: 38 Issue: 16 Pages: 1447-1461

    • DOI

      10.1002/jcc.24785

    • Peer Reviewed / Acknowledgement Compliant
    • Data Source
      KAKENHI-PLANNED-26119006, KAKENHI-PROJECT-16K07286
  • [Journal Article] Hybrid Approach for Biological Structure Modeling: Cryo-electron Microscopy and X-ray Free Electron Laser Data2017

    • Author(s)
      宮下 治, タマ フロハンス
    • Journal Title

      Seibutsu Butsuri

      Volume: 57 Issue: 2 Pages: 090-094

    • DOI

      10.2142/biophys.57.090

    • NAID

      130005509479

    • ISSN
      0582-4052, 1347-4219
    • Language
      Japanese
    • Peer Reviewed / Acknowledgement Compliant / Open Access
    • Data Source
      KAKENHI-PLANNED-26119006, KAKENHI-PROJECT-16K07286, KAKENHI-PROJECT-17K07305
  • [Journal Article] Hybrid approach for structural modeling of biological systems from X-ray free electron laser diffraction patterns2016

    • Author(s)
      Atsushi Tokuhisa, Slavica Jonic, Florence Tama, Osamu Miyashita
    • Journal Title

      Journal of Structural Biology

      Volume: 194-3 Issue: 3 Pages: 325-336

    • DOI

      10.1016/j.jsb.2016.03.009

    • Peer Reviewed / Acknowledgement Compliant / Int'l Joint Research
    • Data Source
      KAKENHI-PROJECT-26870852, KAKENHI-PLANNED-26119006
  • [Journal Article] Local thermodynamics of the water molecules around single- and double-stranded DNA studied by grid inhomogeneous solvation theory2016

    • Author(s)
      Nakano M, Tateishi-Karimata H, Tanaka S, Tama F, Miyashita O, Nakano S, and Sugimoto N
    • Journal Title

      CHEMICAL PHYSICS LETTERS

      Volume: 660 Pages: 250-255

    • DOI

      10.1016/j.cplett.2016.08.032

    • Peer Reviewed / Acknowledgement Compliant
    • Data Source
      KAKENHI-PLANNED-26119006, KAKENHI-PROJECT-16H02283, KAKENHI-PROJECT-26460035, KAKENHI-PROJECT-26810094
  • [Journal Article] Thermodynamic Properties of Water Molecules in the Presence of Cosolute Depend on DNA Structure: A Study Using Grid Inhomogeneous Solvation Theory2015

    • Author(s)
      M. Nakano, H. Tateishi-Karimata, S. Tanaka, F. Tama, O. Miyashita, S. Nakano, N. Sugimoto
    • Journal Title

      Nucl. Acids Res.

      Volume: 43 Pages: 10114-10125

    • DOI

      10.1093/nar/gkv1133

    • Peer Reviewed / Acknowledgement Compliant / Open Access
    • Data Source
      KAKENHI-PROJECT-26460035, KAKENHI-PROJECT-26810094, KAKENHI-PLANNED-26119006, KAKENHI-PROJECT-26620138
  • [Journal Article] Hybrid Electron Microscopy Normal Mode Analysis graphical interface and protocol2014

    • Author(s)
      Sorzano CO, de la Rosa-Trevin JM, Tama F, Jonic S.
    • Journal Title

      J Struct Biol.

      Volume: 188 Issue: 2 Pages: 134-141

    • DOI

      10.1016/j.jsb.2014.09.005

    • Peer Reviewed / Acknowledgement Compliant
    • Data Source
      KAKENHI-PLANNED-26119006
  • [Presentation] Flexible fitting methods and applications2020

    • Author(s)
      Florence Tama
    • Organizer
      EMBO workshop, CEM3DIP 2020: Single particle cryoEM of macromolecular-assemblies and cellular tomography
    • Invited / Int'l Joint Research
    • Data Source
      KAKENHI-PROJECT-17K07305
  • [Presentation] Hybrid modeling approaches to study structures and dynamics of biological systems.2019

    • Author(s)
      Florence Tama
    • Organizer
      63rd Annual Meeting of the Biophysical Society.
    • Invited / Int'l Joint Research
    • Data Source
      KAKENHI-PROJECT-17K07305
  • [Presentation] Hybrid approaches to reveal structure and dynamics of large biological complexes from single molecule experiments2019

    • Author(s)
      Florence Tama
    • Organizer
      American Chemical Society National Meeting
    • Invited / Int'l Joint Research
    • Data Source
      KAKENHI-PROJECT-17K07305
  • [Presentation] Modeling conformational transitions of biomolecules from cryo-EM data2019

    • Author(s)
      Florence Tama
    • Organizer
      French Electron Microscopie Society meeting
    • Invited / Int'l Joint Research
    • Data Source
      KAKENHI-PROJECT-17K07305
  • [Presentation] Integrative modeling to characterize structure and dynamics of biomolecules from single molecule experiments2019

    • Author(s)
      Florence Tama
    • Organizer
      Integrative structural biology meeting
    • Invited / Int'l Joint Research
    • Data Source
      KAKENHI-PROJECT-17K07305
  • [Presentation] Hybrid modeling approaches to study structures and dynamics of biological systems.2018

    • Author(s)
      Florence Tama
    • Organizer
      Annual Meeting of Biophysical Society of Japan
    • Invited
    • Data Source
      KAKENHI-PROJECT-17K07305
  • [Presentation] Computational tools to characterize structure and dynamics of biomolecular systems from single molecule experiments2018

    • Author(s)
      Tama Florence
    • Organizer
      American Chemical Society National Meeting
    • Invited / Int'l Joint Research
    • Data Source
      KAKENHI-PLANNED-26119006
  • [Presentation] Hybrid modeling approaches to study structures and dynamics of biological systems2018

    • Author(s)
      Tama Florence
    • Organizer
      Coarse-Grained Modeling of Structure and Dynamics of Biomacromolecules Workshop
    • Invited / Int'l Joint Research
    • Data Source
      KAKENHI-PLANNED-26119006
  • [Presentation] Hybrid modeling approaches to study structures and dynamics of biological systems2018

    • Author(s)
      Tama Florence
    • Organizer
      63rd Annual Meeting of the Biophysical Society
    • Invited / Int'l Joint Research
    • Data Source
      KAKENHI-PLANNED-26119006
  • [Presentation] Computational tools to characterize structure and dynamics of biomolecular systems from single molecule experiments2018

    • Author(s)
      Florence Tama
    • Organizer
      Laue Langevin Institute, Grenoble, France
    • Invited
    • Data Source
      KAKENHI-PROJECT-17K07305
  • [Presentation] Hybrid modeling approaches to study structures and dynamics of biological systems2018

    • Author(s)
      Tama Florence
    • Organizer
      Second workshop on Advances in Theory and Computation of Complex Systems - Biological Systems.
    • Invited / Int'l Joint Research
    • Data Source
      KAKENHI-PLANNED-26119006
  • [Presentation] Hybrid modeling approaches to study structures and dynamics of biological systems.2018

    • Author(s)
      Florence Tama
    • Organizer
      Coarse-Grained Modeling of Structure and Dynamics of Biomacromolecules Workshop. Telluride USA
    • Invited
    • Data Source
      KAKENHI-PROJECT-17K07305
  • [Presentation] Computational tools to characterize structure and dynamics of biomolecular systems from single molecule experiments.2018

    • Author(s)
      Florence Tama
    • Organizer
      American Chemical Society National Meeting
    • Invited / Int'l Joint Research
    • Data Source
      KAKENHI-PROJECT-17K07305
  • [Presentation] Hybrid modeling approaches to study structures and dynamics of biological systems2018

    • Author(s)
      Florence Tama
    • Organizer
      Second workshop on Advances in Theory and Computation of Complex Systems - Biological Systems. Nanjing, China
    • Invited
    • Data Source
      KAKENHI-PROJECT-17K07305
  • [Presentation] Computational tools to characterize structure and dynamics of biomolecular systems from single molecule experiments2017

    • Author(s)
      Florence Tama
    • Organizer
      Statistics and Algorithms for Biology, INRA, Toulouse, France
    • Invited
    • Data Source
      KAKENHI-PROJECT-17K07305
  • [Presentation] Computational tools to characterize structure and dynamics of biomolecular systems from single molecule experiments. Statistics and Algorithms for Biology2017

    • Author(s)
      Tama Florence
    • Organizer
      Seminar at INRA, Toulouse, France
    • Invited / Int'l Joint Research
    • Data Source
      KAKENHI-PLANNED-26119006
  • [Presentation] Computational tools to characterize structure and dynamics of biomolecular systems from single molecule experiments2017

    • Author(s)
      Tama Florence
    • Organizer
      Seminar at Laue Langevin Institute, Grenoble, France
    • Invited / Int'l Joint Research
    • Data Source
      KAKENHI-PLANNED-26119006
  • [Presentation] Computational tools to characterize structure and dynamics of biomolecular systems from single molecule experiments2017

    • Author(s)
      Florence Tama
    • Organizer
      Biophysical Society of Japan Meeting
    • Invited
    • Data Source
      KAKENHI-PROJECT-17K07305
  • [Presentation] Computational tools to characterize structure and dynamics of biomolecular systems from single molecule experiments2017

    • Author(s)
      Tama Florence
    • Organizer
      Biophysical Society of Japan
    • Invited
    • Data Source
      KAKENHI-PLANNED-26119006
  • [Presentation] Hybrid approaches to characterize structure and dynamics of biomolecular systems from single molecule experiments2016

    • Author(s)
      Tama Florence
    • Organizer
      日本蛋白質科学会
    • Place of Presentation
      福岡国際会議場・福岡県福岡市
    • Year and Date
      2016-06-07
    • Invited
    • Data Source
      KAKENHI-PLANNED-26119006
  • [Presentation] Hybrid approaches to characterize structure and dynamics of biomolecular systems from single molecule experiments2016

    • Author(s)
      Tama Florence
    • Organizer
      Telluride Workshop
    • Place of Presentation
      Telluride Colorado・USA
    • Year and Date
      2016-07-25
    • Invited / Int'l Joint Research
    • Data Source
      KAKENHI-PLANNED-26119006
  • [Presentation] Coarse-Grained Modeling of Structure and Dynamics of Biomacromolecules 3.

    • Author(s)
      Osamu Miyashita, Atsushi Tokuhisa, Florence Tama
    • Organizer
      Telluride Workshop on Coarse-grained modeling of structure and dynamics of biomolecules, Telluride
    • Place of Presentation
      Telluride Science Research Center, Telluride, Collorado, USA
    • Year and Date
      2014-08-04 – 2014-08-08
    • Invited
    • Data Source
      KAKENHI-PLANNED-26119006
  • 1.  Sugita Yuji (80311190)
    # of Collaborated Projects: 2 results
    # of Collaborated Products: 1 results
  • 2.  Kohda Daisuke (80186618)
    # of Collaborated Projects: 1 results
    # of Collaborated Products: 1 results
  • 3.  安藤 敏夫 (50184320)
    # of Collaborated Projects: 1 results
    # of Collaborated Products: 0 results
  • 4.  白川 昌宏 (00202119)
    # of Collaborated Projects: 1 results
    # of Collaborated Products: 0 results
  • 5.  西田 紀貴 (50456183)
    # of Collaborated Projects: 1 results
    # of Collaborated Products: 0 results
  • 6.  塚崎 智也 (80436716)
    # of Collaborated Projects: 1 results
    # of Collaborated Products: 0 results
  • 7.  甲斐荘 正恒 (20137029)
    # of Collaborated Projects: 1 results
    # of Collaborated Products: 0 results
  • 8.  稲垣 冬彦 (70011757)
    # of Collaborated Projects: 1 results
    # of Collaborated Products: 0 results
  • 9.  宮下 治 (10620528)
    # of Collaborated Projects: 1 results
    # of Collaborated Products: 8 results
  • 10.  RAKERS CHRISTIN
    # of Collaborated Projects: 1 results
    # of Collaborated Products: 0 results
  • 11.  田中 成典
    # of Collaborated Projects: 0 results
    # of Collaborated Products: 1 results
  • 12.  徳久 淳師
    # of Collaborated Projects: 0 results
    # of Collaborated Products: 1 results

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