CoDe-DTI: Collaborative Deep Learning-based Drug-Target Interaction Prediction. - Nobuaki Yasuo; Yusuke Nakashima; Masakazu Sekijima (BIBM, 2018)

Compound property enhancement by virtual compound synthesis. - Naoki Arai; Shunsuke Yoshikawa; Nobuaki Yasuo; Ryunosuke Yoshino; Masakazu Sekijima (J. Bioinform. Comput. Biol., 2018)

Improved Method of Structure-Based Virtual Screening via Interaction-Energy-Based Learning. - Nobuaki Yasuo; Masakazu Sekijima (J. Chem. Inf. Model., 2019)

Determination of LQR weights by Bayesian optimization method using multiple earthquake waves. - Kou Miyamoto; Nobuaki Yasuo; Yinli Chen; Daiki Sato; Jinhua She (IECON, 2020)

MERMAID: an open source automated hit-to-lead method based on deep reinforcement learning. - Daiki Erikawa; Nobuaki Yasuo; Masakazu Sekijima (J. Cheminformatics, 2021)

An Improved Model for Predicting Compound Retrosynthesizability Using Machine Learning. - Mami Ozawa; Nobuaki Yasuo; Masakazu Sekijima (BIBE, 2022)

Screening for Inhibitors of Main Protease in SARS-CoV-2: In Silico and In Vitro Approach Avoiding Peptidyl Secondary Amides. - Kazuki Z. Yamamoto; Nobuaki Yasuo; Masakazu Sekijima (J. Chem. Inf. Model., 2022)

IEV2Mol: Molecular Generative Model Considering Protein-Ligand Interaction Energy Vectors. - Mami Ozawa; Shogo Nakamura; Nobuaki Yasuo; Masakazu Sekijima (J. Chem. Inf. Model., 2024)

Mothra: Multiobjective de novo Molecular Generation Using Monte Carlo Tree Search. - Takamasa Suzuki; Dian Ma; Nobuaki Yasuo; Masakazu Sekijima (J. Chem. Inf. Model., 2024)

DiffInt: A Diffusion Model for Structure-Based Drug Design with Explicit Hydrogen Bond Interaction Guidance. - Masami Sako; Nobuaki Yasuo; Masakazu Sekijima (J. Chem. Inf. Model., 2025)

Innovations in mathematical modeling, AI, and optimization techniques. - Masahito Ohue; Nobuaki Yasuo; Masami Takata (J. Supercomput., 2025)