Oshima Hiraku

オシマヒラク | Oshima Hiraku

Affiliation and department：
Job title： Associate Professor

Research field (3)： Nutrition and health science , Bio-, chemical, and soft-matter physics , Biophysics

Research keywords (6)： Molecular dynamics simulation , Drug discovery , Protein , 液体論 , 複雑ネットワーク , 生物物理

Research theme for competitive and other funds (3)：

Papers (40)：

Jaewoon Jung, Kiyoshi Yagi, Cheng Tan, Hiraku Oshima, Takaharu Mori, Isseki Yu, Yasuhiro Matsunaga, Chigusa Kobayashi, Shingo Ito, Diego Ugarte La Torre, et al. GENESIS 2.1: High-Performance Molecular Dynamics Software for Enhanced Sampling and Free-Energy Calculations for Atomistic, Coarse-Grained, and Quantum Mechanics/Molecular Mechanics Models. The Journal of Physical Chemistry B. 2024
Yasuhiro Matsunaga, Motoshi Kamiya, Hiraku Oshima, Jaewoon Jung, Shingo Ito, Yuji Sugita. Use of multistate Bennett acceptance ratio method for free-energy calculations from enhanced sampling and free-energy perturbation. Biophysical Reviews. 2022. 14. 1503-1512
Daiki Matsubara, Kento Kasahara, Hisham M. Dokainish, Hiraku Oshima, Yuji Sugita. Modified Protein-Water Interactions in CHARMM36m for Thermodynamics and Kinetics of Proteins in Dilute and Crowded Solutions. MOLECULES. 2022. 27. 17. 5726
Hiraku Oshima, Yuji Sugita. Modified Hamiltonian in FEP Calculations for Reducing the Computational Cost of Electrostatic Interactions. Journal of Chemical Information and Modeling. 2022
Kento Kasahara, Suyong Re, Grzegorz Nawrocki, Hiraku Oshima, Chiemi Mishima-Tsumagari, Yukako Miyata-Yabuki, Mutsuko Kukimoto-Niino, Isseki Yu, Mikako Shirouzu, Michael Feig, et al. Reduced efficacy of a Src kinase inhibitor in crowded protein solution. Nature Communications. 2021. 12. 1. 4099

ｍore...

MISC (4)：

Hiraku Oshima. Calculation of Free-Energy Landscape Using the GaREUS Method. PSSJ Archives. 2021. 14. e105
尾嶋拓, 李秀栄, 新津藍, 杉田有治. 分子動力学ソフトウェアGENESISを用いたタンパク質-リガンド結合の自由エネルギー計算. シミュレーション. 2021. 40. 22-28
Yuji Sugita, Motoshi Kamiya, Hiraku Oshima, Suyong Re. Replica-Exchange Methods for Biomolecular Simulations. Methods in Molecular Biology. 2019. 155-177
Hiraku Oshima, Takashi Odagaki. Effects of network structure on associative memory. Modelling Perception with Artificial Neural Networks. 2011. 134-148

Lectures and oral presentations (5)：

Developments and applications of generalized-ensemble methods for free-energy analysis of protein-ligand binding
(2020)
Free-energy analysis of protein-ligand binding pose using generalized ensemble methods
(The 57th Annual Meeting of the Biophysical Society of Japan 2019)
リガンド・蛋白質構造変化を考慮した自由エネルギー計算法の開発と応用
(近畿化学協会コンピュータ化学部会公開講演会(第101回例会) 2018)
蛋白質構造変化を考慮したリガンド結合自由エネルギー計算法の開発
(CBI 2017年大会 2017)
タンパク質の熱安定性への糖の影響
(日本物理学会第69回年次大会 2014)

Education (2)：

Professional career (1)：

Work history (10)：

2023/04 - 現在 University of Hyogo, Graduate School of Science
2021/04 - 2023/03 兵庫県立大学大学院情報科学研究科鷲津仁志研究室理研クロスアポイントメント准教授
2019/10 - 2023/03 神戸大学大学院システム情報学研究科非常勤講師
2018/04 - 2023/03 理化学研究所計算科学研究センター特別研究員
2018/04 - 2023/03 RIKEN Center for Biosystems Dynamics Research Research Scientist

Show all

Awards (1)：

2020/07 - 日本蛋白質科学会第20回日本蛋白質科学会年会若手奨励賞優秀賞 Developments and applications of generalized-ensemble methods for free-energy analysis of protein-ligand binding

Association Membership(s) (3)：

PROTEIN SCIENCE SOCIETY OF JAPAN , THE BIOPHYSICAL SOCIETY OF JAPAN , THE PHYSICAL SOCIETY OF JAPAN

※ Researcher’s information displayed in J-GLOBAL is based on the information registered in researchmap. For details, see here.

Return to Previous Page