Tama Florence ＴＡＭＡＦＬＯＲＥＮＣＥ

… Alternative Names

Researcher Number	20648191
Other IDs	https://orcid.org/0000-0003-2021-5618
Affiliation (Current)	2020: 名古屋大学, 理学研究科, 教授 2020: 国立研究開発法人理化学研究所, 計算科学研究センター, チームリーダー
Affiliation (based on the past Project Information) *help	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 Structural biochemistry Except Principal Investigator Complex systems / Biophysics
Keywords	Principal Investigator XFEL / Biomolecules / structure / dynamics / 2D images / 3D structure / single molecules / molecular shapes / database / single-particle … More Except Principal Investigator … More

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Host Researcher
- Host Researcher
  
  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 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: -
- 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 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
[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 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
- 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 inhibition.2018
- Author(s)
  Ashutosh Srivastava, Tsuyoshi Hirota, Stephan Irle and Florence Tama
- Journal Title
  
  Proteins
  
  Volume: 86 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 Pages: 3401-3401
- DOI
  10.3390/ijms19113401
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-16K07286, KAKENHI-PROJECT-17K07305, KAKENHI-PLANNED-26119006
[Journal Article] 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
  
  Journal of Synchrotron Radiation
  
  Volume: 25 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 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 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 images.2018
- Author(s)
  Tiwari Sandhya P.、Tama Florence、Miyashita Osamu
- Journal Title
  
  BMC Bioinformatics
  
  Volume: 19 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 Comput Chem
  
  Volume: 38 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
  
  Biophysics
  
  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
  
  J Struct Biol.
  
  Volume: 194-3 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
  
  Chem. Phys. Lett.
  
  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
  
  Nucleic 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 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: 2 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. RAKERS CHRISTIN

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
10. TATEISHI Hisae

# of Collaborated Projects: 0 results

# of Collaborated Products: 2 results
11. 廣田毅

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results
12. 宮下治

# of Collaborated Projects: 0 results

# of Collaborated Products: 10 results
13. 田中成典

# of Collaborated Projects: 0 results

# of Collaborated Products: 2 results
14. 杉本直己

# of Collaborated Projects: 0 results

# of Collaborated Products: 2 results
15. 城地保昌

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results
16. 徳久淳師

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results

Tama Florence ＴＡＭＡ ＦＬＯＲＥＮＣＥ

TAMA FLORENCE タマ フロハンス

Research Projects

Research Products

Co-Researchers

Database of Molecular Shapes and Diffraction Patterns for X-ray Free Electron Laser Data AnalysisPrincipal Investigator

Principal Investigator

Project Period (FY)

Research Category

Research Field

Research Institution

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Host Researcher

Host Researcher

Project Period (FY)

Research Category

Research Field

Research Institution

Support activities aimed at international network formation in the research area of dynamic structural life sciences

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

Molecular dynamics simulations of protein complexes based on multi-resolution models

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

[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)

Total Pages

Publisher

ISBN

Data Source

[Journal Article] Reconstruction of low-resolution molecular structures from simulated atomic force microscopy images2020

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Computational Protocol for Assessing the Optimal Pixel Size to Improve the Accuracy of Single-particle Cryo-electron Microscopy Maps2020

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Integrative/Hybrid Modeling Approaches for Studying Biomolecules2020

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Cryo-Cooling Effect on DHFR Crystal Studied by Replica-Exchange Molecular Dynamics Simulations2019

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Acceleration of cryo-EM Flexible Fitting for Large Biomolecular Systems by Efficient Space Partitioning2019

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Conformational dynamics of human protein kinase CK2α and its effect on function and inhibition.2018

Author(s)

Journal Title

DOI

NAID

Data Source

[Journal Article] Role of Computational Methods in Going beyond X-ray Crystallography to Explore Protein Structure and Dynamics2018

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Single-particle XFEL 3D reconstruction of ribosome-size particles based on Fourier slice matching: requirements to reach subnanometer resolution2018

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Gaussian mixture model for coarse-grained modeling from XFEL2018

Author(s)

Journal Title

DOI

Tama Florence ＴＡＭＡＦＬＯＲＥＮＣＥ

TAMA FLORENCE タマフロハンス