Comprehensive 3D-RISM analysis of the hydration of small molecule binding sites in ligand-free protein structures. - Takashi Yoshidome; Mitsunori Ikeguchi; Masateru Ohta (J. Comput. Chem., 2020)

kGCN: a graph-based deep learning framework for chemical structures. - Ryosuke Kojima; Shoichi Ishida; Masateru Ohta; Hiroaki Iwata; Teruki Honma; Yasushi Okuno (J. Cheminformatics, 2020)

High-Precision Atomic Charge Prediction for Protein Systems Using Fragment Molecular Orbital Calculation and Machine Learning. - Koichiro Kato; Tomohide Masuda; Chiduru Watanabe; Naoki Miyagawa; Hideo Mizouchi; Shumpei Nagase; Kikuko Kamisaka; Kanji Oshima; Satoshi Ono; Hiroshi Ueda; Atsushi Tokuhisa; Ryo Kanada; et al. (J. Chem. Inf. Model., 2020)

Effect of Water Molecules on the Activating S810L Mutation of the Mineralocorticoid Receptor. - Kei Takedomi; Masateru Ohta; Toru Ekimoto; Mitsunori Ikeguchi (J. Chem. Inf. Model., 2021)

gr Predictor: A Deep Learning Model for Predicting the Hydration Structures around Proteins. - Kosuke Kawama; Yusaku Fukushima; Mitsunori Ikeguchi; Masateru Ohta; Takashi Yoshidome (J. Chem. Inf. Model., 2022)

Selective Inhibitor Design for Kinase Homologs Using Multiobjective Monte Carlo Tree Search. - Tatsuya Yoshizawa; Shoichi Ishida; Tomohiro Sato; Masateru Ohta; Teruki Honma; Kei Terayama (J. Chem. Inf. Model., 2022)

AI-driven molecular generation of not-patented pharmaceutical compounds using world open patent data. - Yugo Shimizu; Masateru Ohta; Shoichi Ishida; Kei Terayama; Masanori Osawa; Teruki Honma; Kazuyoshi Ikeda (J. Cheminformatics, 2023)

Conformational Selectivity of ITK Inhibitors: Insights from Molecular Dynamics Simulations. - Naoki Ogawa; Masateru Ohta; Mitsunori Ikeguchi (J. Chem. Inf. Model., 2023)

Quantitative Structure-Activity Relationships for Human Galectin-3 Inhibitors: Insights from Quantum Chemical Interaction Energy Terms. - Tomohide Masuda; Chiduru Watanabe; Koichiro Kato; Teruki Honma; Masateru Ohta; Mitsunori Ikeguchi (J. Chem. Inf. Model., 2025)