Okamoto Yuko

オカモトユウコウ | Okamoto Yuko

Affiliation and department：
Job title： Professor
Homepage URL (2)： https://www.phys.nagoya-u.ac.jp/list/HPtemplate/HPtemplate_Okamoto_j.pdf , https://www.phys.nagoya-u.ac.jp/en/list/HPtemplate/HPtemplate_Okamoto_e.pdf

Research keywords (5)： replica-exchange method , simulated tempering , multicanonical algorithm , generalized-ensemble algorithm , computer simulation of protein folding

Research theme for competitive and other funds (14)：

2013 - 2018 生体分子集団および人工分子集団の相互作用と大規模構造転換
2013 - 2018 拡張アンサンブル法による蛋白質への小分子結合機構の研究
2013 - 2015 拡張アンサンブル密度汎関数分子動力学法によるATP加水分解の研究
2011 - 2014 Prediction of protein-ligand binding structures by generalized-ensemble simulations
2008 - 2013 Development of molecular simulation methods that enhance structural fluctuations and free energy calculations

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Papers (261)：

Yukihiro Itoh, Yusuke Nakashima, Shuichiro Tsukamoto, Takashi Kurohara, Miki Suzuki, Yoshitake Sakae, Masayuki Oda, Yuko Okamoto, Takayoshi Suzuki. N⁺-C-H···O Hydrogen bonds in protein-ligand complexes. Scientific Reports. 2019. 9. 1
Tachi Yuhei, Okamoto Yuko, Okumura Hisashi. Conformational Change of Amyloid-beta 40 in Association with Binding to GM1-Glycan Cluster. SCIENTIFIC REPORTS. 2019. 9
N. Nishikawa, Y. Sakae, T. Gouda, Y. Tsujimura, Y. Okamoto. Structural Analysis of a Trimer of β2-Microgloblin Fragment by Molecular Dynamics Simulations. Biophysical Journal. 2019. 116. 781-790
Tachi Yuhei, Sato Sota, Yoneya Makoto, Fujita Makoto, Okamoto Yuko. Two polyhedral frameworks of an M12L24 spherical complex revealed by replica-exchange molecular dynamics simulations. CHEMICAL PHYSICS LETTERS. 2019. 714. 185-189
M. Shimizu, Y. Kajikawa, K. Kuwajima, C.M. Dobson, Y. Okamoto. Determination of the Structural Ensemble of the Molten Globule State of a Protein by Computer Simulations. Proteins: Structure, Function, and Bioinformatics. 2019. in press

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MISC (255)：

Tachi Yuhei, Okamoto Yuko, Okumura Hisashi. Conformational properties of an artificial GM1 glycan cluster based on a metal-ligand complex. JOURNAL OF CHEMICAL PHYSICS. 2018. 149. 13
Ito Shingo, Wang Ying, Okamoto Yuko, Irle Stephan. Quantum chemical replica-exchange umbrella sampling molecular dynamics simulation reveal the formation mechanism of iron phthalocyanine iron and phthalonitrile. JOURNAL OF CHEMICAL PHYSICS. 2018. 149. 7
Shingo Ito, Dmitri G. Fedorov, Yuko Okamoto, Stephan Irle. Implementation of replica-exchange umbrella sampling in GAMESS. Computer Physics Communications. 2018. 228. 152-162
Shuichiro Tsukamoto, Yoshitake Sakae, Yukihiro Itoh, Takayoshi Suzuki, Yuko Okamoto. Computational analysis for selectivity of histone deacetylase inhibitor by replica-exchange umbrella sampling molecular dynamics simulations. Journal of Chemical Physics. 2018. 148. 12
Shin Kawano, Yasushi Tamura, Rieko Kojima, Siqin Bala, Eri Asai, Agnès H. Michel, Benoît Kornmann, Isabelle Riezman, Howard Riezman, Yoshitake Sakae, et al. Structure-function insights into direct lipid transfer between membranes by Mmm 1-Mdm 12 of ERMES. Journal of Cell Biology. 2018. 217. 3. 959-974

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Books (37)：

Optimizations of protein force fields in Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes
Springer Berlin Heidelberg 2019 ISBN:9783642285530
Optimizations of protein force fields in Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes
Springer Berlin Heidelberg 2019 ISBN:9783319958422
Conformational Dynamics of Oligosaccharides Characterized by Paramagnetism-Assisted NMR Spectroscopy in Conjunction with Molecular Dynamics Simulation, in Biochemical Roles of Eukaryotic Cell Surface Macromolecules
Springer 2015 ISBN:9783319112794
Protein folding simulations by generalized-ensemble algorithms, in Advances in Experimental Medicine and Biology
Springer, Berlin 2013 ISBN:9783319029702
Enhanced sampling algorithms, in Biomolecular Simulations: Methods and Protocols
Humana Press 2013

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Lectures and oral presentations (239)：

Enhanced sampling techniques for classical and quantum molecular simulations
(The 5th International Conference on Molecular Simulation (ICMS 2019) 2019)
Enhanced sampling methods for complex spin and molecular systems
(Molecular Simulation 2019 Meeting 2019)
Enhanced sampling simulations for water and biomolecules
(The 10th Toyota RIKEN International Workshop on Science of Life Phenomena Woven by Water and Biomolecules 2019)
Enhanced sampling methods for classical and quantum simulations
(The 4th International Conference on Computational Science and Engineering (ICCSE-4) 2019)
Enhanced sampling techniques for free energy calculations
(Free Energy Calculations: Entering the Fourth Decade of Adventure in Chemistry and Biophysics 2019)

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Professional career (4)：

理学士ー理学修士 (ブラウン大学)
理学博士 (コーネル大学)
Bachelor of Science - Master of Science (B.S.-M.S.) (Brown University)
Doctor of Philosophy (Ph.D.) (Cornell University)

Work history (17)：

2011/04/01 - 現在 Nagoya University Graduate School of Engineering Center for Computational Science Professor
2010/06/01 - 現在 Nagoya University Information Technology Center High Performance Computing division Professor
2007/02/01 - 現在 Nagoya University Structural Biology Research Center Professor
2007/02/01 - 現在 Nagoya University Graduate School of Science Structural Biology Research Center Professor
2005/04/01 - 現在 Professor, Department of Physics, Graduate School of Science, Nagoya University

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Association Membership(s) (9)：

American Chemical Society , American Physical Society , 理論化学研究会 , 分子科学会 , Protein Society of Japan , The Molecular Simulation Society of Japan , Chemical Society of Japan , Biophysical Society of Japan , Physical Society of Japan

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