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Miyashita Osamu  宮下 治

… Alternative Names

MIYASHITA Osamu  宮下 治

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Researcher Number 10620528
Other IDs
  • ORCIDhttps://orcid.org/0000-0002-2530-5674
Affiliation (Current) 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, 上級研究員
Affiliation (based on the past Project Information) *help 2018 – 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, 上級研究員
2016 – 2017: 国立研究開発法人理化学研究所, 計算科学研究機構, 上級研究員
2013 – 2014: 独立行政法人理化学研究所, 計算科学研究機構, 上級研究員
Review Section/Research Field
Principal Investigator
Basic Section 43020:Structural biochemistry-related / Complex systems / Structural biochemistry / Biophysics
Except Principal Investigator
Transformative Research Areas, Section (II) / Complex systems
Keywords
Principal Investigator
分子動力学シミュレーション / 動的構造解析 / 生体高分子 / ハイブリッドアプローチ / タンパク質 / クライオ電子顕微鏡 / シミュレーション / モデリング / 構造分布 / データ融合シミュレーション … More / 構造解析 / タンパク質-膜間相互作用 / 可視紫外吸収スペクトル帰属 / プロトン化 / 電子状態 / 化学反応解析 / 量子古典混合計算 / 脂質膜 / ベイズ統計 / 電子顕微鏡 / ハイブリッドモデリング / フィッティング / 構造モデリング / 計算構造生物学 / X線結晶構造解析 / データベース解析 / 結晶構造 / 計算機構造生物 / 計算機生物物理 … More
Except Principal Investigator
integrative modeling / protein dynamics / integrative modelling / intrinsically disordered / MD simulations / Protein dynamics / 構造モデリング / タンパク質ダイナミクス / シリアルフェムト秒結晶構造解析 / 動的構造解析 / 蛋白質結晶構造解析 / X線溶液散乱 / X線結晶構造解析 / 動的構造 / 結晶構造解析 / 温度ジャンプ / 溶液散乱 / 時分割実験 / X線自由電子レーザー Less
  • Research Projects

    (6 results)
  • Research Products

    (65 results)
  • Co-Researchers

    (11 People)
  •  クライオ電子顕微鏡画像データとシミュレーションの融合による生体高分子動的構造解析Principal Investigator

    • Principal Investigator
      宮下 治
    • Project Period (FY)
      2024 – 2026
    • Research Category
      Grant-in-Aid for Scientific Research (C)
    • Review Section
      Basic Section 43020:Structural biochemistry-related
    • Research Institution
      Institute of Physical and Chemical Research
  •  Integrating data and simulation for dynamic structural biology

    • 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
  •  Unraveling Protein Chemical Reaction Dynamics through Molecular SimulationsPrincipal Investigator

    • Principal Investigator
      Miyashita Osamu
    • Project Period (FY)
      2020 – 2023
    • 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
  •  Reaction initiation techniques in time-resolved experiments

    • Principal Investigator
      Nango Eriko
    • Project Period (FY)
      2019 – 2023
    • Research Category
      Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)
    • Review Section
      Complex systems
    • Research Institution
      Tohoku University
      Institute of Physical and Chemical Research
  •  New approaches for biostructure modeling from low-resolution experimental dataPrincipal Investigator

    • Principal Investigator
      Miyashita Osamu
    • Project Period (FY)
      2016 – 2019
    • Research Category
      Grant-in-Aid for Scientific Research (C)
    • Research Field
      Structural biochemistry
    • Research Institution
      Institute of Physical and Chemical Research
  •  Effect of Crystal Environment on Protein Structures: Molecular Dynamics Simulations and Database AnalysisPrincipal Investigator

    • Principal Investigator
      MIYASHITA Osamu
    • Project Period (FY)
      2013 – 2014
    • Research Category
      Grant-in-Aid for Research Activity Start-up
    • Research Field
      Biophysics
    • Research Institution
      The Institute of Physical and Chemical Research

All 2024 2023 2022 2021 2020 2019 2018 2017 2016 2015

All Journal Article Presentation Book

  • [Book] Hybrid Methods for Macromolecular Modeling by Molecular Mechanics Simulations with Experimental Data2018

    • Author(s)
      Osamu Miyashita, Florence Tama
    • Total Pages
      19
    • Publisher
      Springer
    • Data Source
      KAKENHI-PROJECT-16K07286
  • [Journal Article] Structure determination using high-order spatial correlations in single-particle X-ray scattering2024

    • Author(s)
      Zhao Wenyang、Miyashita Osamu、Nakano Miki、Tama Florence
    • Journal Title

      IUCrJ

      Volume: 11 Issue: 1 Pages: 92-108

    • DOI

      10.1107/s2052252523009831

    • Peer Reviewed / Open Access
    • Data Source
      KAKENHI-PLANNED-20H05453
  • [Journal Article] Molecular size dependence on achievable resolution from XFEL single-particle 3D reconstruction2023

    • Author(s)
      Miki Nakano, Osamu Miyashita, Florence Tama
    • Journal Title

      Structural Dynamics

      Volume: 10 Issue: 2 Pages: 024101-024101

    • DOI

      10.1063/4.0000175

    • Peer Reviewed / Open Access
    • Data Source
      KAKENHI-PROJECT-18K14642, KAKENHI-PLANNED-20H05453
  • [Journal Article] Advancing cryo-electron microscopy data analysis through accelerated simulation-based flexible fitting approaches2023

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

      Current Opinion in Structural Biology

      Volume: 82 Pages: 102653-102653

    • DOI

      10.1016/j.sbi.2023.102653

    • Peer Reviewed
    • Data Source
      KAKENHI-PLANNED-20H05453
  • [Journal Article] MDSPACE: Extracting Continuous Conformational Landscapes from Cryo-EM Single Particle Datasets Using 3D-to-2D Flexible Fitting based on Molecular Dynamics Simulation2023

    • Author(s)
      Vuillemot Remi、Mirzaei Alex、Harastani Mohamad、Hamitouche Ilyes、Frechin Leo、Klaholz Bruno P.、Miyashita Osamu、Tama Florence、Rouiller Isabelle、Jonic Slavica
    • Journal Title

      Journal of Molecular Biology

      Volume: 435 Issue: 9 Pages: 167951-167951

    • DOI

      10.1016/j.jmb.2023.167951

    • Peer Reviewed / Int'l Joint Research
    • Data Source
      KAKENHI-PLANNED-20H05453
  • [Journal Article] A hybrid approach to study large conformational transitions of biomolecules from single particle XFEL diffraction data2022

    • Author(s)
      Asi Han、Dasgupta Bhaskar、Nagai Tetsuro、Miyashita Osamu、Tama Florence
    • Journal Title

      Frontiers in Molecular Biosciences

      Volume: 9 Pages: 1-15

    • DOI

      10.3389/fmolb.2022.913860

    • Peer Reviewed / Open Access
    • Data Source
      KAKENHI-PLANNED-20H05453
  • [Journal Article] NMMD: Efficient Cryo-EM Flexible Fitting Based on Simultaneous Normal Mode and Molecular Dynamics atomic displacements2022

    • Author(s)
      Vuillemot Remi、Miyashita Osamu、Tama Florence、Rouiller Isabelle、Jonic Slavica
    • Journal Title

      Journal of Molecular Biology

      Volume: 434 Issue: 7 Pages: 167483-167483

    • DOI

      10.1016/j.jmb.2022.167483

    • Peer Reviewed / Open Access / Int'l Joint Research
    • Data Source
      KAKENHI-PLANNED-20H05453
  • [Journal Article] High-resolution structure of phosphoketolase from Bifidobacterium longum determined by cryo-EM single-particle analysis2022

    • Author(s)
      Nakata Kunio、Miyazaki Naoyuki、Yamaguchi Hiroki、Hirose Mika、Kashiwagi Tatsuki、Kutumbarao Nidamarthi H.V.、Miyashita Osamu、Tama Florence、Miyano Hiroshi、Mizukoshi Toshimi、Iwasaki Kenji
    • Journal Title

      Journal of Structural Biology

      Volume: 214 Issue: 2 Pages: 107842-107842

    • DOI

      10.1016/j.jsb.2022.107842

    • Peer Reviewed / Open Access
    • Data Source
      KAKENHI-PLANNED-20H05453
  • [Journal Article] Identifying Structural Properties of Proteins from X-ray Free Electron Laser Diffraction Patterns2022

    • Author(s)
      Olaya Paula、Caino-Lores Silvina、Lama Vanessa、Patel Ria、Rorabaugh Ariel Keller、Miyashita Osamu、Tama Florence、Taufer Michela
    • Journal Title

      2022 IEEE 18th International Conference on e-Science (e-Science)

      Volume: - Pages: 21-31

    • DOI

      10.1109/escience55777.2022.00017

    • Peer Reviewed / Int'l Joint Research
    • Data Source
      KAKENHI-PLANNED-20H05453
  • [Journal Article] Three-dimensional structure determination of gold nanotriangles in solution using X-ray free-electron laser single-particle analysis2022

    • Author(s)
      Nakano Miki、Miyashita Osamu、Joti Yasumasa、Suzuki Akihiro、Mitomo Hideyuki、Niida Yoshiya、Yang Ying、Yumoto Hirokatsu、Koyama Takahisa、Tono Kensuke、Ohashi Haruhiko、Yabashi Makina、Ishikawa Tetsuya、BESSHO YOSHITAKA、Ijiro Kuniharu、Nishino Yoshinori、Tama Florence
    • Journal Title

      Optica

      Volume: 9 Issue: 7 Pages: 776-784

    • DOI

      10.1364/optica.457352

    • Peer Reviewed / Open Access / Int'l Joint Research
    • Data Source
      KAKENHI-PUBLICLY-20H05433, KAKENHI-PROJECT-21K03497, KAKENHI-PROJECT-22K19908, KAKENHI-PROJECT-22K19929, KAKENHI-PUBLICLY-21H05863, KAKENHI-PROJECT-19H05627, KAKENHI-PROJECT-21H01736, KAKENHI-PROJECT-18K14642, KAKENHI-PLANNED-20H05453, KAKENHI-PUBLICLY-22H04741
  • [Journal Article] Protocol for Retrieving Three-Dimensional Biological Shapes for a Few XFEL Single-Particle Diffraction Patterns2021

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

      Journal of Chemical Information and Modeling

      Volume: 61 Issue: 8 Pages: 4108-4119

    • DOI

      10.1021/acs.jcim.1c00602

    • Peer Reviewed / Open Access
    • Data Source
      KAKENHI-PLANNED-20H05453
  • [Journal Article] Reconstruction of Three-Dimensional Conformations of Bacterial ClpB from High-Speed Atomic-Force-Microscopy Images2021

    • Author(s)
      Bhaskar Dasgupta, Osamu Miyashita, Takayuki Uchihashi and Florence Tama
    • Journal Title

      Frontiers in in Molecular Biosciences: Biological Modeling and Simulation

      Volume: 8 Pages: 704274-704274

    • DOI

      10.3389/fmolb.2021.704274

    • Peer Reviewed / Open Access
    • Data Source
      KAKENHI-PUBLICLY-20H04669, KAKENHI-PLANNED-20H05453, KAKENHI-PUBLICLY-21H00393, KAKENHI-PROJECT-21H01772
  • [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] 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] 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] 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] 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] Effect of the crystal environment on side-chain conformational dynamics in Cyanovirin-N investigated through crystal and solution molecular dynamics simulations2016

    • Author(s)
      Ahlstrom LS, Vorontsov II, Shi J, Miyashita O
    • Journal Title

      PLoS One

      Volume: 12 Issue: 1 Pages: e0170337-e0170337

    • DOI

      10.1371/journal.pone.0170337

    • Peer Reviewed / Acknowledgement Compliant / Open Access / Int'l Joint Research
    • Data Source
      KAKENHI-PLANNED-26119006, KAKENHI-PROJECT-16K07286
  • [Presentation] Integrative/Hybrid Modeling Approaches for Dynamic Structural Biology2024

    • Author(s)
      Osamu Miyashita
    • Organizer
      Workshop on "Program for Promoting Researches on the Supercomputer Fugaku”
    • Invited
    • Data Source
      KAKENHI-PLANNED-20H05453
  • [Presentation] Integrative/Hybrid Modeling Approaches for Dynamic Structural Biology2023

    • Author(s)
      Osamu Miyashita
    • Organizer
      “Molecular Movies” International Symposium 2023
    • Invited / Int'l Joint Research
    • Data Source
      KAKENHI-PLANNED-20H05453
  • [Presentation] 構造生物学へのハイブリッドアプローチ: シミュレーションと実験データの融合2023

    • Author(s)
      宮下治
    • Organizer
      日本蛋白質科学会大会
    • Invited
    • Data Source
      KAKENHI-PLANNED-20H05453
  • [Presentation] Integrative/Hybrid Modeling Approaches for Dynamic Structural Biology2023

    • Author(s)
      Osamu Miyashita
    • Organizer
      Multi-scale Molecular Dynamics Simulation and Machine Learning of Biomolecular Systems
    • Invited / Int'l Joint Research
    • Data Source
      KAKENHI-PLANNED-20H05453
  • [Presentation] XFELを用いた単粒子解析で復元された 分子構造の解像度における分子サイズの影響2023

    • Author(s)
      中野 美紀、宮下 治、Tama Florence
    • Organizer
      第36回日本放射光学会年会・放射光科学合同シンポジウム
    • Data Source
      KAKENHI-PLANNED-20H05453
  • [Presentation] 構造生物学へのハイブリッドアプローチ: シミュレーションと実験データの融合2022

    • Author(s)
      宮下治
    • Organizer
      物性研短期研究会:理論と実験との密な協働
    • Invited
    • Data Source
      KAKENHI-PLANNED-20H05453
  • [Presentation] Reconstruction algorithm of low-resolution three-dimensional conformations of biomolecules from atomic force microscopy images2022

    • Author(s)
      Osamu Miyashita, Bhaskar Dasgupta, and Florence Tama
    • Organizer
      ACS Spring 2022
    • Int'l Joint Research
    • Data Source
      KAKENHI-PLANNED-20H05453
  • [Presentation] 3D structural determination of proteins from fluctuation X-ray scattering data2022

    • Author(s)
      Zhao Wenyang, Miyashita Osamu, Tama Florence
    • Organizer
      The 60th Annual Meeting of the Biophysical Society of Japan
    • Int'l Joint Research
    • Data Source
      KAKENHI-PLANNED-20H05453
  • [Presentation] Molecular size effect on the single-particle analysis using X-ray free electron laser2022

    • Author(s)
      Nakano Miki, Miyashita Osamu, Tama Florence
    • Organizer
      The 60th Annual Meeting of the Biophysical Society of Japan
    • Int'l Joint Research
    • Data Source
      KAKENHI-PLANNED-20H05453
  • [Presentation] X線自由電子レーザー単粒子解析を使用した溶液中の金ナノ粒子の三次元構造決定2022

    • Author(s)
      中野美紀, 宮下治, 城地保昌, 鈴木明大, 西野吉則, and Tama Florence
    • Organizer
      第35回日本放射光学会年会・放射光科学合同シンポジウム
    • Data Source
      KAKENHI-PLANNED-20H05453
  • [Presentation] Automated Density Extraction of Isomorphous Difference Map and Occupancy-estimation for Conformer Fitting2022

    • Author(s)
      Srinivasa Raghavan Sriram, Miyashita Osamu , Tama Florence
    • Organizer
      The 60th Annual Meeting of the Biophysical Society of Japan
    • Int'l Joint Research
    • Data Source
      KAKENHI-PLANNED-20H05453
  • [Presentation] 構造生物学へのハイブリッドアプローチ: シミュレーションと実験データの融合2022

    • Author(s)
      宮下治
    • Organizer
      The 95th Annual Meeting of the Japanese Biochemical Society
    • Invited
    • Data Source
      KAKENHI-PLANNED-20H05453
  • [Presentation] Automated Density Extraction of Isomorphous Difference map and Occupancy-estimation for Conformer Fitting2022

    • Author(s)
      Srinivasa Raghavan Sriram, Miyashita Osamu, Tama Florence
    • Organizer
      令和4年度新学術領域研究「高速分子動画」シンポジウム
    • Data Source
      KAKENHI-PLANNED-20H05453
  • [Presentation] Molecular size effect on the single-particle 3D structure reconstruction analysis using X-ray free electron laser2022

    • Author(s)
      Miki Nakano, Osamu Miyashita, and Florence Tama
    • Organizer
      The 4th R-CCS International Symposium
    • Int'l Joint Research
    • Data Source
      KAKENHI-PLANNED-20H05453
  • [Presentation] Automated Density Extraction of Isomorphous Difference Map and Occupancy-estimation for Conformer Fitting2022

    • Author(s)
      Srinivasa Raghavan Sriram, Miyashita Osamu, Tama Florence
    • Organizer
      Molecular Movies International Symposium 2022
    • Int'l Joint Research
    • Data Source
      KAKENHI-PLANNED-20H05453
  • [Presentation] Requirement for 3D-reconstruction of biomolecule structure from single particle analysis using X-ray free electron laser diffraction images2021

    • Author(s)
      M Nakano, F Tama, O Miyashita
    • Organizer
      The 3rd R-CCS International Symposium
    • Int'l Joint Research
    • Data Source
      KAKENHI-PLANNED-20H05453
  • [Presentation] Modelling multiple types of three-dimensional hexameric conformations of bacterial heat-shock protein ClpB from low-resolution AFM image2021

    • Author(s)
      B Dasgupta, O Miyashita, F Tama
    • Organizer
      The 3rd R-CCS International Symposium
    • Int'l Joint Research
    • Data Source
      KAKENHI-PLANNED-20H05453
  • [Presentation] Retrieving potential three-dimensional biological shape matches from a small number of two-dimensional single particle XFEL diffraction patterns2021

    • Author(s)
      S Tiwari, F Tama, O Miyashita
    • Organizer
      The 3rd R-CCS International Symposium
    • Int'l Joint Research
    • Data Source
      KAKENHI-PLANNED-20H05453
  • [Presentation] Retrieving potential three-dimensional biological shape matches from a small number of two-dimensional single particle XFEL diffraction patterns2020

    • Author(s)
      S Tiwari, F Tama, O Miyashita
    • Organizer
      Protein Society Meeting of Japan
    • Data Source
      KAKENHI-PLANNED-20H05453
  • [Presentation] Protocol for Assessing the Optimal Pixel Size to Improve the Accuracy of Single-Particle Cryo-Electron Microscopy Maps2020

    • Author(s)
      O Miyashita, S Tiwari, F Tama
    • Organizer
      CBI学会2020年大会
    • Data Source
      KAKENHI-PLANNED-20H05453
  • [Presentation] Simulation study of tree dimensional reconstruction of ribosome from Xray free electron laser diffraction patterns2020

    • Author(s)
      M Nakano, F Tama, O Miyashita
    • Organizer
      Protein Society Meeting of Japan
    • Data Source
      KAKENHI-PLANNED-20H05453
  • [Presentation] 構造生物学へのハイブリッドアプローチ: シミュレーションと実験データの融合2020

    • Author(s)
      O Miyashita
    • Organizer
      第 1 回ピコバイオロジー研究会
    • Invited
    • Data Source
      KAKENHI-PLANNED-20H05453
  • [Presentation] Reconstruction of Low-resolution (Bio) Molecular Structures from Simulated Atomic Force Microscopy Images2020

    • Author(s)
      宮下治
    • Organizer
      The 1st International Conference on Big Data and Machine Learning in Microscopy
    • Invited / Int'l Joint Research
    • Data Source
      KAKENHI-PROJECT-16K07286
  • [Presentation] Hybrid Approach for Biomolecular Structure Modeling2020

    • Author(s)
      宮下治
    • Organizer
      2nd R-CCS international symposium
    • Int'l Joint Research
    • Data Source
      KAKENHI-PROJECT-16K07286
  • [Presentation] Hybrid Structure Modeling of Biomolecules from Cryo-EM Data2019

    • Author(s)
      宮下治
    • Organizer
      日本顕微鏡学会
    • Invited
    • Data Source
      KAKENHI-PROJECT-16K07286
  • [Presentation] Cryo-cooling effect on DHFR crystal studied by replica-exchange molecular dynamics simulations2019

    • Author(s)
      Osamu Miyashita
    • Organizer
      BioXFEL International Conference
    • Int'l Joint Research
    • Data Source
      KAKENHI-PROJECT-16K07286
  • [Presentation] Hybrid Approach for Structural Biology: Simulation and Experimental Data2019

    • Author(s)
      宮下治
    • Organizer
      CBI 学会
    • Invited
    • Data Source
      KAKENHI-PROJECT-16K07286
  • [Presentation] XFEL単粒子実験データ解析アルゴリズムの開発2019

    • Author(s)
      宮下治
    • Organizer
      PCXSS Workshop
    • Invited
    • Data Source
      KAKENHI-PROJECT-16K07286
  • [Presentation] Hybrid Approach for Structural Biology: Simulation and Experimental Data2019

    • Author(s)
      宮下治
    • Organizer
      CBI 学会
    • Invited
    • Data Source
      KAKENHI-PLANNED-19H05781
  • [Presentation] クライオEMデータを活用した生体分子ハイブリッド構造モデリング2019

    • Author(s)
      宮下治
    • Organizer
      近畿化学協会コンピュータ化学部会 公開講演会
    • Invited
    • Data Source
      KAKENHI-PROJECT-16K07286
  • [Presentation] XFEL単粒子観測実験データ解析アルゴリズムの開発2018

    • Author(s)
      宮下治
    • Organizer
      放射光学会若手研究会
    • Invited
    • Data Source
      KAKENHI-PROJECT-16K07286
  • [Presentation] Dynamics hidden within X-ray crystallographic data2018

    • Author(s)
      Osamu Miyashita
    • Organizer
      Telluride Workshop: Coarse-Grained Modeling of Structure and Dynamics of Biomacromolecules
    • Invited / Int'l Joint Research
    • Data Source
      KAKENHI-PROJECT-16K07286
  • [Presentation] 構造解析へのハイブリッドアプローチ:電子顕微鏡とX線自由電子レーザーからの実験データの活用2018

    • Author(s)
      宮下治
    • Organizer
      第 1 回水和ナノ構造研究会
    • Invited
    • Data Source
      KAKENHI-PROJECT-16K07286
  • [Presentation] 構造解析へのハイブリッドアプローチ:電子顕微鏡とX線結晶解析実験データの活用2018

    • Author(s)
      宮下治
    • Organizer
      日本結晶学会 2018年度年会
    • Invited
    • Data Source
      KAKENHI-PROJECT-16K07286
  • [Presentation] 計算構造生物学による生体超分子構造解析2018

    • Author(s)
      宮下治
    • Organizer
      クライオ電顕解析における情報解析技術ワークショップ
    • Invited
    • Data Source
      KAKENHI-PROJECT-16K07286
  • [Presentation] 構造解析へのハイブリッドアプローチ : 電子顕微鏡とX線自由電子レーザーからの実験データの活用2017

    • Author(s)
      宮下治
    • Organizer
      第4回 大型実験施設とスーパーコンピュータとの連携利用シンポジウム-生体物質のダイナミクス-
    • Invited
    • Data Source
      KAKENHI-PROJECT-16K07286
  • [Presentation] XFEL単粒子実験データ解析アルゴリズムの開発2017

    • Author(s)
      宮下治
    • Organizer
      PCXSS Workshop
    • Invited
    • Data Source
      KAKENHI-PROJECT-16K07286
  • [Presentation] 計算機シミュレーションと実験データの融合利用2017

    • Author(s)
      宮下治
    • Organizer
      XFEL構造生物ミーティング
    • Place of Presentation
      SACLA,兵庫県佐用郡
    • Invited
    • Data Source
      KAKENHI-PROJECT-16K07286
  • [Presentation] Computational Structure Modeling from Cryo-EM Data2017

    • Author(s)
      宮下治
    • Organizer
      Dynamic Structural Biology Symposium
    • Invited
    • Data Source
      KAKENHI-PROJECT-16K07286
  • [Presentation] Structure Modeling from Cryo-EM Data using Flexible Fitting Approach2016

    • Author(s)
      宮下治
    • Organizer
      日本生物物理学会
    • Place of Presentation
      つくば国際会議場,茨城県つくば市
    • Year and Date
      2016-11-25
    • Invited
    • Data Source
      KAKENHI-PROJECT-16K07286
  • [Presentation] 電子顕微鏡データを活用した構造解析へのハイブリッドアプローチ2016

    • Author(s)
      宮下治
    • Organizer
      理研シンポジウム「クライオ電顕に期待すること」
    • Place of Presentation
      理研横浜,神奈川県横浜市
    • Invited
    • Data Source
      KAKENHI-PROJECT-16K07286
  • [Presentation] Effect of Crystal Packing on Protein Conformations and Dynamics2015

    • Author(s)
      宮下治
    • Organizer
      Large-scale biological simulations using supercomputers
    • Place of Presentation
      理化学研究所計算科学研究機構
    • Year and Date
      2015-04-02
    • Invited
    • Data Source
      KAKENHI-PROJECT-25891031
  • 1.  庄司 光男 (00593550)
    # of Collaborated Projects: 2 results
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  • 2.  篠田 恵子 (80646951)
    # of Collaborated Projects: 2 results
    # of Collaborated Products: 0 results
  • 3.  Nango Eriko (90376947)
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  • 4.  清水 伸隆 (20450934)
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  • 5.  大和田 成起 (90725962)
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  • 6.  TAMA FLORENCE (20648191)
    # of Collaborated Projects: 1 results
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  • 7.  AHLSTROM Logan
    # of Collaborated Projects: 1 results
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  • 8.  中野 美紀
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  • 9.  杉田 有治
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  • 10.  内橋 貴之
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  • 11.  鈴木 明大
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