Kamiya Narutoshi

カミヤナルトシ | Kamiya Narutoshi

Affiliation and department：

Research field (1)： Biophysics

Research theme for competitive and other funds (10)：

2021 - 2024 クチナーゼCut190のCa2+結合に伴う動的構造変化とPET分解分子機構の解明
2020 - 2023 Complex structure and affinity prediction among cancer vaccine peptides and immune related proteins
2016 - 2019 Accurate predictions of complex structure and affinity between proteins and drugs
2012 - 2017 Elucidation of information-processing mechanisms during transcription cycle using computational and information sciences
2013 - 2016 Development of a complex structure prediction method between proteins using binding free-energy as a scoring function

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Papers (71)：

Gert-Jan Bekker, Kanji Oshima, Mitsugu Araki, Yasushi Okuno, Narutoshi Kamiya. Binding Mechanism between Platelet Glycoprotein and Cyclic Peptide Elucidated by McMD-Based Dynamic Docking. Journal of Chemical Information and Modeling. 2024. 64. 10. 4158-4167
Gert-Jan Bekker, Yoshifumi Fukunishi, Junichi Higo, Narutoshi Kamiya. Binding Mechanism of Riboswitch to Natural Ligand Elucidated by McMD-Based Dynamic Docking Simulations. ACS Omega. 2024. 9. 3412-3422
Ryo Kanada, Atsushi Tokuhisa, Yusuke Nagasaka, Shingo Okuno, Koichiro Amemiya, Shuntaro Chiba, Gert-Jan Bekker, Narutoshi Kamiya, Koichiro Kato, Yasushi Okuno. Enhanced Coarse-Grained Molecular Dynamics Simulation with a Smoothed Hybrid Potential Using a Neural Network Model. Journal of Chemical Theory and Computation. 2023. 20. 1. 7-17
Junichi Higo, Gert-Jan Bekker, Narutoshi Kamiya, Ikuo Fukuda, Yoshifumi Fukunishi. Binding free-energy landscapes of small molecule binder and non-binder to FMN riboswitch: All-atom molecular dynamics. Biophysics and Physicobiology. 2023. 20. e200047
Gert-Jan Bekker, Nobutaka Numoto, Maki Kawasaki, Takahiro Hayashi, Saaya Yabuno, Yuko Kozono, Takeyuki Shimizu, Haruo Kozono, Nobutoshi Ito, Masayuki Oda, et al. Elucidation of binding mechanism, affinity and complex structure between mWT1 tumor-associated antigen peptide and HLA-A*24:02. Protein Science. 2023. 32. 10. e4775

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MISC (6)：

Gert-Jan Bekker, Narutoshi Kamiya. Thermal Stability Estimation of Single Domain Antibodies Using Molecular Dynamics Simulations. Computer-Aided Antibody Design. 2023. 151-163
Gert-Jan Bekker, Narutoshi Kamiya. Dynamic Docking Using Multicanonical Molecular Dynamics: Simulating Complex Formation at the Atomistic Level. Methods in Molecular Biology. 2021. 187-202
Masayuki Oda, Nobutaka Numoto, Gert-Jan Bekker, Narutoshi Kamiya, Fusako Kawai. Cutinases from thermophilic bacteria (actinomycetes): From identification to functional and structural characterization. Methods in Enzymology. 2021. 159-185
神谷成敏. Thermal Stability Estimation of Single-Domain Antibodies by Molecular Dynamics Simulations. 熱測定. 2020. 47. 4
白木琢磨, 神谷成敏, 陣上久人. 内在性リガンドの結合様式からみた核内受容体PPARγの活性化機構. 蛋白質核酸酵素. 2005. 50. 13. 1660-1665

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