Miyashita Osamu

ミヤシタオサム | Miyashita Osamu

Affiliation and department：
Job title： Senior Scientist

Research field (2)： Biophysics , Structural biochemistry

Research theme for competitive and other funds (5)：

2024 - 2029 Integrating data and simulation for dynamic structural biology
2020 - 2024 分子シミュレーションによるタンパク質化学反応ダイナミクスの解明
2019 - 2024 時分割実験のための多様な反応誘起システムの開発
2016 - 2020 New approaches for biostructure modeling from low-resolution experimental data
2013 - 2015 Effect of Crystal Environment on Protein Structures: Molecular Dynamics Simulations and Database Analysis

Papers (70)：

Xuan Wu, Osamu Miyashita, Florence Tama. Modeling Conformational Transitions of Biomolecules from Atomic Force Microscopy Images using Normal Mode Analysis. The journal of physical chemistry. B. 2024
Wenyang Zhao, Osamu Miyashita, Miki Nakano, Florence Tama. Structure determination using high-order spatial correlations in single-particle X-ray scattering. IUCrJ. 2024. 11. Pt 1. 92-108
Osamu Miyashita, Florence Tama. Advancing cryo-electron microscopy data analysis through accelerated simulation-based flexible fitting approaches. Current opinion in structural biology. 2023. 82. 102653-102653
Rémi Vuillemot, Alex Mirzaei, Mohamad Harastani, Ilyes Hamitouche, Léo Fréchin, Bruno P Klaholz, Osamu Miyashita, Florence Tama, Isabelle Rouiller, Slavica Jonic. MDSPACE: Extracting Continuous Conformational Landscapes from Cryo-EM Single Particle Datasets Using 3D-to-2D Flexible Fitting based on Molecular Dynamics Simulation. Journal of molecular biology. 2023. 435. 9. 167951-167951
Miki Nakano, Osamu Miyashita, Florence Tama. Molecular size dependence on achievable resolution from XFEL single-particle 3D reconstruction. Structural dynamics (Melville, N.Y.). 2023. 10. 2. 024101-024101

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MISC (16)：

Nakano Miki, Miyashita Osamu, Jonic Slavica, Tokuhisa Atsushi, Tama Florence. Protocol for three-dimensional structure reconstruction using simulated XFEL coherent diffraction data. Meeting Abstracts of the Physical Society of Japan. 2018. 73. 0. 3078-3078
Jonic S, Miyashita O, Callebaut I. Editorial: Hybrid Biomolecular Modeling. Frontiers in molecular biosciences. 2018. 5. 98-98
中野美紀, 建石寿枝, 田中成典, FLORENCE Tama, FLORENCE Tama, 宮下治, 杉本直己. 共溶質存在下におけるDNA水和水の熱力学的性質の解析. 分子シミュレーション討論会講演要旨集. 2017. 31st. 64-65
A. Srivastava, O. Miyashita, F. Tama. Computational investigation of binding and dynamics in Tom20-mitochondrial targeting signal complex. EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS. 2017. 46. S232-S232
Tokuhisa Atsushi, Miyashita Osamu, Tama Florence. 3P084 Examination of ab initio structural modeling for the pattern matching method using X-ray free electron laser(01E. Protein: Measurement & Analysis,Poster,The 52nd Annual Meeting of the Biophysical Society of Japan(BSJ2014)). Seibutsu Butsuri. 2014. 54. 1. S262

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Books (3)：

Hybrid Methods for Macromolecular Modeling by Molecular Mechanics Simulations with Experimental Data.
2018
Structure and Function of the Cytochrome c2: Reaction Center Complex from Rhodobacter sphaeroides
Springer, Dordrecht 2009
Coarse-grained normal mode analysis to explore large scale dynamics of biological molecules.
Chapman and Hall/CRC Press, Taylor and Francis Group 2008

Education (2)：

Professional career (1)：

Work history (13)：

2018/04 - 現在 RIKEN Center for Computational Science Senior Scientist
2021/04 - 2022/03 名古屋大学大学院理学研究科非常勤講師
2021/04 - 2021/09 兵庫県立大学非常勤講師
2019/04 - 2020/03 名古屋大学大学院理学研究科非常勤講師
2013/05 - 2018/03 RIKEN Advanced Institute for Computational Science Senior Scientist

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