Nobutaka Numoto, Fumiya Kondo, Gert-Jan Bekker, Zengwei Liao, Mitsuaki Yamashita, Akira Iida, Nobutoshi Ito, Narutoshi Kamiya, Masayuki Oda. Structural dynamics of the Ca2+-regulated cutinase towards structure-based improvement of PET degradation activity. International Journal of Biological Macromolecules. 2024. 281. 136597-136597
Mitsugu Araki, Toru Ekimoto, Kazuhiro Takemura, Shigeyuki Matsumoto, Yunoshin Tamura, Hironori Kokubo, Gert-Jan Bekker, Tsutomu Yamane, Yuta Isaka, Yukari Sagae, et al. Molecular Dynamics Unveils Multiple-Site Binding of Inhibitors with Reduced Activity on the Surface of Dihydrofolate Reductase. Journal of the American Chemical Society. 2024
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