The Effect of Conformational Flexibility on Binding Free Energy Estimation between Kinases and Their Inhibitors. - Mitsugu Araki; Narutoshi Kamiya; Miwa Sato; Masahiko Nakatsui; Takatsugu Hirokawa; Yasushi Okuno (J. Chem. Inf. Model., 2016)

Machine learning accelerates MD-based binding pose prediction between ligands and proteins. - Kei Terayama; Hiroaki Iwata; Mitsugu Araki; Yasushi Okuno; Koji Tsuda (Bioinform., 2018)

Improving the Accuracy of Protein-Ligand Binding Mode Prediction Using a Molecular Dynamics-Based Pocket Generation Approach. - Mitsugu Araki; Hiroaki Iwata; Biao Ma; Atsuto Fujita; Kei Terayama; Yukari Sagae; Fumie Ono; Koji Tsuda; Narutoshi Kamiya; Yasushi Okuno (J. Comput. Chem., 2018)

Exhaustive search of the configurational space of heat-shock protein 90 with its inhibitor by multicanonical molecular dynamics based dynamic docking. - Gert-Jan Bekker; Mitsugu Araki; Kanji Oshima; Yasushi Okuno; Narutoshi Kamiya (J. Comput. Chem., 2020)

Accurate Binding Configuration Prediction of a G-Protein-Coupled Receptor to Its Antagonist Using Multicanonical Molecular Dynamics-Based Dynamic Docking. - Gert-Jan Bekker; Mitsugu Araki; Kanji Oshima; Yasushi Okuno; Narutoshi Kamiya (J. Chem. Inf. Model., 2021)

Structure-Based de Novo Molecular Generator Combined with Artificial Intelligence and Docking Simulations. - Biao Ma; Kei Terayama; Shigeyuki Matsumoto; Yuta Isaka; Yoko Sasakura; Hiroaki Iwata; Mitsugu Araki; Yasushi Okuno (J. Chem. Inf. Model., 2021)

Extraction of protein dynamics information from cryo-EM maps using deep learning. - Shigeyuki Matsumoto; Shoichi Ishida; Mitsugu Araki; Takayuki Kato; Kei Terayama; Yasushi Okuno (Nat. Mach. Intell., 2021)

Protein-ligand binding affinity prediction of cyclin-dependent kinase-2 inhibitors by dynamically averaged fragment molecular orbital-based interaction energy. - Kenichiro Takaba; Chiduru Watanabe; Atsushi Tokuhisa; Yoshinobu Akinaga; Biao Ma; Ryo Kanada; Mitsugu Araki; Yasushi Okuno; Yusuke Kawashima; Hirotomo Moriwaki; Norihito Kawashita; Teruki Honma; et al. (J. Comput. Chem., 2022)

Binding Mechanism between Platelet Glycoprotein and Cyclic Peptide Elucidated by McMD-Based Dynamic Docking. - Gert-Jan Bekker; Kanji Oshima; Mitsugu Araki; Yasushi Okuno; Narutoshi Kamiya (J. Chem. Inf. Model., 2024)