Yoshidome Takashi

ヨシドメタカシ | Yoshidome Takashi

Affiliation and department：
Job title： Associate Professor
Homepage URL (2)： https://sites.google.com/view/takashiyoshidome-wp/%E3%83%9B%E3%83%BC%E3%83%A0 , http://web.tohoku.ac.jp/mathphys/en/

Research field (2)： Biophysics , Bio-, chemical, and soft-matter physics

Research keywords (8)：液体論 , タンパク質 , 溶媒和・水和 , マニフォールドラーニング , 電子顕微鏡 , コヒーレントX線回折イメージング , ガラス転移 , 自由エネルギーランドスケープ

Research theme for competitive and other funds (12)：

2022 - 2028 次世代放射光X線ナノCT計測の確立と展開
2024 - 2027 「高速・高精度な水和理論」を用いたリガンド結合予測の精度向上
2023 - 2025 タンパク質水和の「深層学習モデル」の展開:水和熱力学量の高速計算
2022 - 2024 生体分子ダイナミクスの高解像度解析を実現する「4次元イメージング法」の確立
2021 - 2024 A Construction of Drug Design Theory based on the Hydration of Proteins

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Papers (44)：

Takashi Yoshidome. Four-dimensional imaging for cryo-electron microscopy experiments using molecular simulations and manifold learning. Journal of Computational Chemistry. 2023. 45. 11. 738-751
Takashi Yoshidome. Mechanism of a high free-energy transduction efficiency of Bacillus PS3 F1-ATPase from the perspective of solvent entropy. Journal of Molecular Liquids. 2023. 123346(1)-123346(9)
Yuki Hishikawa, Hiroki Noya, Satoru Nagatoishi, Takashi Yoshidome, Basudev Maity, Kouhei Tsumoto, Satoshi Abe, Takafumi Ueno. Elucidating Conformational Dynamics and Thermostability of Designed Aromatic Clusters by Using Protein Cages. Chemistry - A European Journal. 2023. 29. 34. e202300488
Kosuke Kawama, Yusaku Fukushima, Mitsunori Ikeguchi, Masateru Ohta, Takashi Yoshidome. gr Predictor: A Deep Learning Model for Predicting the Hydration Structures around Proteins. Journal of Chemical Information and Modeling. 2022. 62. 4460-4473
Takashi Yoshidome. Simple-Fluid Model for Accurate Reproduction of Hydration Entropy. Journal of the Physical Society of Japan. 2022. 91. 9. 094802-1-094802-6

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MISC (59)：

Takashi Yoshidome, Yuki Sekiguchi, Tomotaka Oroguchi, Masayoshi Nakasako, Mitsunori Ikeguchi. Reconstruction of Three-Dimensional Structures of a Protein with Software ENMA and EMC Algorithm: A Simulation for XFEL-CXDI Experiment. BIOPHYSICAL JOURNAL. 2017. 112. 3. 288A-288A
Takashi Yoshidome, Toru Ekimoto, Nobuyuki Matubayasi, Yuichi Harano, Masahiro Kinoshita, Mitsunori Ikeguchi. An Accurate and Efficient, Computational Method for the Hydration Free Energy of Large and Complex Molecules. BIOPHYSICAL JOURNAL. 2016. 110. 3. 328A-329A
Yoshidome T., Oroguchi T., Nakasako M., Ikeguchi M. 7aAM-5 Imaging analysis using a new classification protocol of projection images based on the manifold. Meeting abstracts of the Physical Society of Japan. 2014. 69. 2. 188-188
Yoshidome T., Oroguchi T., Nakasako M., Ikeguchi M. 30aPS-101 A novel classification protocol of projection images : Toward analysis of dynamics of targets with coherent x-ray diffraction imaging. Meeting abstracts of the Physical Society of Japan. 2014. 69. 1. 423-423
Takashi Yoshidome, Tomotaka Oroguchi, Masayoshi Nakasako, Mitsunori Ikeguchi. Classification Protocol of Projection Images by Manifold: Toward Analysis of Dynamics of Particles with Coherent X-Ray Diffraction Imaging. BIOPHYSICAL JOURNAL. 2014. 106. 2. 384A-384A

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Books (1)：

Lectures and oral presentations (100)：

Deep-Learning Model For Fast And Accurate Computation Of Hydration Structures Around Proteins
(Biomolecular Horizons 2024 2024)
Manifold-Learning Approach to Material Data: Application to Experimental Data of Liquid Substances and Porous Structural Data
(12th Liquid Matter Conference 2024)
Deep Learning-Based Water Molecule Displacement Prediction Method for Improving the Accuracy of Drug Discovery Docking Software
(IUPAB2024 2024)
Molecular Dynamics Study of the Unfolding Processes of Proteins with Highly Similar Native Structure
(IUPAB2024 2024)
Fast Computational Method for the Hydration Free Energy
(IUPAB2024 2024)

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Professional career (1)：

Committee career (5)：

Awards (6)：

2024/02 - 令和5年度東北大学応用物理学コース卒業研修発表賞(指導した学生が受賞) 機械学習を用いたタンパク質構造変化データの解析
2022/09 - 9th Biophysics and Physicobiology Editors' Choice Award A Measure for the Identification of Preferred Particle Orientations in Cryo-Electron Microscopy Data: A Simulation Study
2021/10 - HPCI利用研究課題第8回成果報告会 HPCI利用研究課題優秀成果賞
2021/03 - 日本生物物理学会北海道支部-東北支部合同例会学生優秀発表賞(指導した学生が受賞) 深層学習の視点に基づいたタンパク質水和分布法の高度化
2019/12 - 第47回構造活性相関シンポジウム SAR Presentation Award (Poster presentation)

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Association Membership(s) (6)：

THE JAPANESE SOCIETY FOR SYNCHROTRON RADIATION RESEARCH , 日本物理学会 , 日本生物物理学会 , Biophysical Society , 日本蛋白質科学会 , 日本薬学会

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