Darai, N., Hengphasatporn, K., Wolschann, P., Wolfinger, M. T., Shigeta, Y., Rungrotmongkol, T., & Harada, R. A Structural Refinement Technique for Protein-RNA Complexes Using Combination of AI-based Modeling and Flexible Docking: A Study of Musashi-1 Protein, Bull. Chem. Soc. Jpn., 96, 677-685, doi: 10.1246/bcsj.20230092, (2023).
Munei, Y., Hengphasatporn, K., Hori, Y., Harada, R., & Shigeta, Y. Determination of the Association between Mesotrione Sensitivity and Conformational Change of 4-Hydroxyphenylpyruvate Dioxygenase via Free-Energy Analyses, J. Agric. Food Chem., 71, 9528-9537, doi: 10.1021/acs.jafc.3c01253, (2023).
Munei, Y., Shigeta, Y., & Harada, R. A Variety of Initial Velocities in Restarting Molecular Dynamics Simulations Promotes Protein Transitions, Chem. Lett., 52, 385-388, doi: 10.1246/cl.230104 (2023).
原田隆平, 森田陸離, 重田育照, 化合物の膜透過プロセスを紐解く自由エネルギー計算手法の開発, 日本薬学会 構造活性相関部会 SAR News, 44, 22-23, https://sar.pharm.or.jp/wp-content/uploads/2023/04/SAR-News-No44.pdf (2023).
Morita, R., Shigeta, Y., & Harada, R. Efficient Screening of Protein-Ligand Complexes in Lipid Bilayers Using LoCoMock Score, J. Comput. Aided Mol. Des. 37, 217-225, doi: 10.1007/s10822-023-00502-8 (2023).
Munei, Y., Hori, Y., Hengphasatporn, K., Harada, R., & Shigeta, 4-hydroxyphenylpyruvate dioxygenase (HPPD)における金属活性中心の力場パラメータの構築とその評価, J. Comput. Chem. Jpn., 21, 82-84, doi: 10.2477/jccj.2023-0003 (2023).
Takahashi, T., Hengphasatporn, K., Harada, R., & Shigeta, 中分子の膜透過性に対する計算手法の検討, J. Comput. Chem. Jpn., 21, 118-122, doi:10.2477/jccj.2023-0007 (2023).
重田育照, 高橋輝行, 満田祐樹, 原田隆平, 第一原理計算と分子動力学計算による膜透過性の評価・推定 , 技術情報協会「ケモインフォマティクスにおけるデータ収集の最適化と解析手法」, 8, 589-599 (2023).
保田拓範, 原田隆平, Parallel Cascade Selection Molecular Dynamics (PaCS-MD) に基づくタンパク質の遷移経路探索, 分子シミュレーション学会誌「アンサンブル」25, 19-27 (2023).
Harada, R., Morita, R., & Shigeta, Y. Free-energy Profiles for Membrane Permeation of Compounds Calculated Using Rare-Event Sampling Methods, J. Chem. Model. Inf. 63, 259-269, doi: 10.1021/acs.jcim.2c01097 (2023).
Nishida, Y., Yanagisawa, S., Morita, R., Shigematsu, H., Shinzawa-Itoh, K., Yuki, H., Ogasawara, S., Shimuta, K., Iwamoto, T., Nakabayashi, C., Matsumura, W., Kato, H., Nagao, T., Qaqorh, T., Takahashi, Y., Yamazaki, S., Kamiya, K., Harada, R., Mizuno, N., Takahashi, H., Akeda, Y., Ohnishi, M., Kumasaka, T., Murata, T., Muramoto, K., Tosha, T., Shiro, Y., Honma, T., Shigeta, Y., Kubo, M., Takashima, S., & Shintani Y. Identifying antibiotics based on structural differences in the conserved allostery from mitochondrial heme-copper oxidases. Nat. Commun., 13, 7591, doi.org/10.1038/s41467-022-34771-y (2022).
Yasuda, T., Morita, R., Shigeta, Y. & Harada, R. Protein Structure Validation Derives a Smart Conformational Search in a Physically Relevant Configurational Subspace. J. Chem. Inf. Model., 62, 6217-6227, doi.org/10.1021/acs.jcim.2c01173 (2022).
Hengphasatporn, K., Harada, R., Wilasluck, P., Deetanya, P., Sukandar, E. R., Chavasiri, W., Suroengrit, A., Boonyasuppayakorn, S., Rungrotmongkol, T., Wangkanont, K. & Shigeta, Y. Promising SARS-CoV-2 Main Protease Inhibitor Ligand-Binding Modes Evaluated Using LB-PaCS-MD/FMO. Sci. Rep. 12, 11891, doi.org/10.1038/s41598-022-22703-1 (2022).
Takumi,T., Yasuda, T., Morita, R., Kim, J., Shigeta, Y., Eroglu, C., Harada, R. & Tsuruta, F. Autism-Associated Mutation in Hevin Induces Endoplasmic Reticulum Stress Through Structural Instability. Sci. Rep. 12, doi.org/10.1038/s41598-022-15784-5 (2022).
Yasuda, T., Morita, R., Shigeta, Y. & Harada, R. The Structural Validation by G-factor Regulates Boost Potentials Employed in Conformational Sampling of Proteins. J. Chem. Inf. Model. 62, 3442-3452, doi.org/10.1021/acs.jcim.2c00573 (2022).
Aida, H., Shigeta, Y. & Harada, R. The Role of ATP in Solubilizing RNA-binding Protein Fused in Sarcoma. Proteins: Struct. Funct. Bioinformat. 90, 1602-1612, doi.org/10.1002/prot.26335 (2022).
Aida, H., Shigeta, Y. & Harada, R. Ligand Binding Path Sampling Based on Parallel Cascade Selection Molecular Dynamics: LB-PaCS-MD. Materials 15, 1490, doi.org/10.3390/ma15041490 (2022).
Yasuda, T., Morita, R., Shigeta, Y. & Harada, R. Histone H3 Inhibits Ubiquitin-Ubiquitin Intermolecular Interactions to Enhance Binding to DNA Methyl Transferase 1. J. Mol. Biol. 434, 167371, doi.org/10.1016/j.jmb.2021.167371 (2022).
Aoyagi, T., Yoshino, R., Mitsuta, Y., Morita, R., Harada, R. & Shigeta, Y. Integrate In Silico Studies on the Role of Nicotinamide Adenine Dinucleotide (NADH) Binding in Activating C-terminal Binding Protein 2 (CtBP2). Chem. Lett. 51, 1-4, doi.org/10.1246/cl.210548 (2022).
Ashida, S.†, Morita, R.†, Shigeta, Y. & Harada, R. Phosphorylation on the Accessory Domain of Yeast Histone Chaperone yNap1 Exposes the Nuclear Export Sequence. Proteins: Struct. Funct. Bioinformat. 9, 317-321, doi.org/10.1002/prot.26240 (2022). †Equally Contributed.
2021
Sladek, V., Harada, R., & Shigeta, Y. Residue Folding Degree - Relationship to Secondary Structure Categories and use as Collective Variable. Int. J. Mol. Sci. 22, 13042, doi:org/ 10.3390/ijms222313042 (2021).
Morita, R., Shigeta, Y. & Harada, R. Structural Variations of Metallothionein with or without Zinc Ions Elucidated by All-Atom Molecular Dynamics Simulations. J. Phys. Chem. B 125, 12712-12717, doi.org/10.1021/acs.jpcb.1c07928 (2021).
Yanagki, K., Mitsuta, Y., Takaoka, K., Takahashi, T., Hengphasatporn, K., Harada, R. & Shigeta, Y. Solubility and Membrane Permeability of Cyclic Dipeptides Approximately Estimated by Quantum Chemistry and Molecular Dynamics Calculations. Chem. Lett. 50, 1964-1967, doi.org/10.1246/cl.210488 (2021).
Morita, R., Shigeta, Y. & Harada, R. A Post-Process to Estimate an Approximated Minimal Free Energy Path Based on Local Centroids. Chem. Phys. Lett. 782, 139003-1-10, doi.org/10.1016/j.cplett.2021.139003 (2021).
Aida, H.†, Morita, R.†, Shigeta, Y. & Harada, R. In Silico Mutational Analyses Reveal Different Ligand-Binding Abilities of Double Pockets of Medaka Fish Taste Receptor Type 1 Essential for Efficient Taste Recognitions. Phys. Chem. Chem. Phys. 23, 20398-20405, doi.org/10.1039/D1CP02876F (2021). †Equally Contributed.
Yasuda, T., Morita, R., Shigeta, Y. & Harada, R. Independent Non-targeted Parallel Cascade Selection Molecular Dynamics (Ino-PaCS-MD) to Enhance the Conformational Sampling of Proteins. J. Chem. Theory Coumput. 50, 162-165, doi.org/10.1021/acs.jctc.1c00558 (2021).
Morita, R., Shigeta, Y., Harada, R. Comprehensive Predictions of Secondary Structures for Comparative Analysis in Different Species. J. Struct. Biol. 213, 107735-1-8, doi.org/10.1016/j.jsb.2021.107735 (2021).
Harada, R., Rare Event Sampling of Proteins Based on Distributed Molecular Dynamics Simulations, Frontier 3, 9-16 (2021).
Yasuda, T., Shigeta, Y. & Harada, R. The Folding of Trp-cage is Regulated by Stochastic Flip of the Side Chain of Tryptophan. Chem. Lett. 50, 162-165, doi.org/10.1246/cl.200699 (2021).
Morita, R., Shigeta, Y. & Harada, R. Rearrangements of Water Molecules in Parallel Cascade Selection Molecular Dynamics Enhance Structural Explorations of Proteins. Bull. Chem. Soc. Jpn. 94, 97-105, doi.org/10.1246/bcsj.20200174 (2021).
Harada, R., Yamaguchi, K, & Shigeta, Y. Enhanced Conformational Sampling Method Based on Anomaly Detection Parallel Cascade Selection Molecular Dynamics: ad-PaCS-MD. J. Chem. Theory. Comput. 16, 6716-6725, doi.org/10.1021/acs.jctc.0c00697 (2020)
Yasuda, T., Shigeta, Y. & Harada, R. Efficient Conformational Sampling of Collective Motions of Proteins with Principal Component Analysis-Based Parallel Cascade Selection Molecular Dynamics. J. Chem. Inf. Model. 60, 4021-4029, doi.org/10.1021/acs.jcim.0c00580 (2020).
Yasuda, T., Shigeta, Y. & Harada, R. The Dynamics of S-adenosyl-methionine and S-adenosyl-homocysteine in Mouse Dnmt1 is Driven by Their Structural Flexibilities. Chem. Lett. 49, 785-788, doi.org/10.1246/cl.200223 (2020).
Morita, R., Nakano, K., Shigeta, Y. & Harada, R. Molecular Mechanism for the Actin-Binding Domain of alpha-Actinin Ain1 Elucidated by Molecular Dynamics Simulations and Mutagenesis Experiments. J. Phys. Chem. B 124, 8495-8503, doi.org/10.1021/acs.jpcb.0c04623 (2020).
Aida, H., Shigeta, Y. & Harada, R. Regenerations of Initial Velocities in Parallel Cascade Selection Molecular Dynamics (PaCS-MD) Enhance the Conformational Transitions of Proteins. Chem. Lett. 49, 798-801, doi.org/10.1246/cl.200196 (2020).
公益財団法人 豊田理化学研究所 豊田理研スカラー（2023）原田 隆平
公益財団法人 日立財団 倉田奨励金（2023）原田 隆平
筑波大学友会賞（2022）岡本 慶乃
第36回 分子シミュレーション討論会 学生優秀発表賞（2022）保田 拓範
第50回 構造活性相関シンポジウム 優秀発表賞（SAR Presentation Award）（2022） 原田 隆平
公益財団法人 住友財団 基礎科学研究助成（2022）原田 隆平
公益財団法人 日揮・実吉奨学会 研究助成制度 （2022）原田 隆平
公益財団法人 三島海雲記念財団 学術研究奨励金 （2022）原田 隆平
筑波大学大学院 理工情報生命学術院 生命地球科学研究群長表彰 （2022）保田 拓範
筑波大学大学院 理工情報生命学術院 生物学位プログラムリーダー表彰（2022）保田 拓範
筑波大学学生奨学金「つくばスカラシップ」（2022）保田 拓範
筑波大学大学院 理工情報生命学術院 生物学位プログラムリーダー表彰（2022）會田 勇斗
日本学術振興会 特別研究員（DC1）特別研究奨励費 （2022）保田 拓範
新学術領域研究「生命金属科学」領域会議 第４回地方巡業（東京）若手優秀研究発表賞 (2021) 森田 陸離
令和三年度 科学技術分野の文部科学大臣表彰 若手科学者賞 （2021）原田 隆平
筑波大学若手教員特別奨励賞（2021）原田 隆平
筑波大学学長表彰（2021）保田 拓範
筑波大学茗渓会賞（2021）今村 彩子
筑波大学若手教員奨励賞（2020）原田 隆平
筑波大学学長表彰（2020）會田 勇斗
筑波大学先導的研究体験プログラム研究発表会優秀賞 （2020）保田 拓範
分子シミュレーション学会学術賞（2019）原田 隆平
日本生物物理学会学生発表賞（2019) 會田 勇斗
生体分子討論会優秀ポスター賞（2019）森田 陸離
日本物理学会若手奨励賞（2019）原田 隆平
日本化学会進歩賞（2018）原田 隆平
日本生物物理学会若手招待講演賞（2016）原田隆平