Prediction of Human Liver Microsomal Stability with Machine Learning. - Yojiro Sakiyama; Hitomi Yuki; Teruki Honma (IC-AI, 2008)

Combining Machine Learning and Pharmacophore-Based Interaction Fingerprint for in Silico Screening. - Tomohiro Sato; Teruki Honma; Shigeyuki Yokoyama (J. Chem. Inf. Model., 2010)

Application of Support Vector Machine to Three-Dimensional Shape-Based Virtual Screening Using Comprehensive Three-Dimensional Molecular Shape Overlay with Known Inhibitors. - Tomohiro Sato; Hitomi Yuki; Daisuke Takaya; Shunta Sasaki; Akiko Tanaka; Teruki Honma (J. Chem. Inf. Model., 2012)

Prediction of Ligand-Induced Structural Polymorphism of Receptor Interaction Sites Using Machine Learning. - Daisuke Takaya; Tomohiro Sato; Hitomi Yuki; Shunta Sasaki; Akiko Tanaka; Shigeyuki Yokoyama; Teruki Honma (J. Chem. Inf. Model., 2013)

Bioisostere Identification by Determining the Amino Acid Binding Preferences of Common Chemical Fragments. - Tomohiro Sato; Noriaki Hashimoto; Teruki Honma (J. Chem. Inf. Model., 2017)

Theoretical Analysis of Activity Cliffs among Benzofuranone-Class Pim1 Inhibitors Using the Fragment Molecular Orbital Method with Molecular Mechanics Poisson-Boltzmann Surface Area (FMO+MM-PBSA) Approach. - Chiduru Watanabe; Hirofumi Watanabe; Kaori Fukuzawa; Lorien J. Parker; Yoshio Okiyama; Hitomi Yuki; Shigeyuki Yokoyama; Hirofumi Nakano; Shigenori Tanaka; Teruki Honma (J. Chem. Inf. Model., 2017)

Force-field parametrization based on radial and energy distribution functions. - Shuntaro Chiba; Yasushi Okuno; Teruki Honma; Mitsunori Ikeguchi (J. Comput. Chem., 2019)

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)

Special Features of COVID-19 in the FMODB: Fragment Molecular Orbital Calculations and Interaction Energy Analysis of SARS-CoV-2-Related Proteins. - Kaori Fukuzawa; Koichiro Kato; Chiduru Watanabe; Yusuke Kawashima; Yuma Handa; Ami Yamamoto; Kazuki Watanabe 005; Tatsuya Ohyama; Kikuko Kamisaka; Daisuke Takaya; Teruki Honma (J. Chem. Inf. Model., 2021)

FMODB: The World's First Database of Quantum Mechanical Calculations for Biomacromolecules Based on the Fragment Molecular Orbital Method. - Daisuke Takaya; Chiduru Watanabe; Shunpei Nagase; Kikuko Kamisaka; Yoshio Okiyama; Hirotomo Moriwaki; Hitomi Yuki; Tomohiro Sato; Noriyuki Kurita; Yoichiro Yagi; Tatsuya Takagi; Norihito Kawashita; et al. (J. Chem. Inf. Model., 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)

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)

FMOe: Preprocessing and Visualizing Package of the Fragment Molecular Orbital Method for Molecular Operating Environment and Its Applications in Covalent Ligand and Metalloprotein Analyses. - Hirotomo Moriwaki; Yusuke Kawashima; Chiduru Watanabe; Kikuko Kamisaka; Yoshio Okiyama; Kaori Fukuzawa; Teruki Honma (J. Chem. Inf. Model., 2024)

Geometry Optimization Using the Frozen Domain and Partial Dimer Approaches in the Fragment Molecular Orbital Method: Implementation, Benchmark, and Applications to Protein Ligand-Binding Sites. - Koji Okuwaki; Naoki Watanabe; Koichiro Kato; Chiduru Watanabe; Naofumi Nakayama; Akifumi Kato; Yuji Mochizuki; Tatsuya Nakano; Teruki Honma; Kaori Fukuzawa (J. Chem. Inf. Model., 2024)

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)

Large language models open new way of AI-assisted molecule design for chemists. - Shoichi Ishida; Tomohiro Sato; Teruki Honma; Kei Terayama (J. Cheminformatics, 2025)