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

Temperature-pressure shuffling outlier flooding method enhances the conformational sampling of proteins. - Ryuhei Harada; Ryunosuke Yoshino; Hiroaki Nishizawa; Yasuteru Shigeta (J. Comput. Chem., 2019)

Pocket to concavity: a tool for the refinement of protein-ligand binding site shape from alpha spheres. - Genki Kudo; Takumi Hirao; Ryunosuke Yoshino; Yasuteru Shigeta; Takatsugu Hirokawa (Bioinform., 2023)

AAp-MSMD: Amino Acid Preference Mapping on Protein-Protein Interaction Surfaces Using Mixed-Solvent Molecular Dynamics. - Genki Kudo; Keisuke Yanagisawa; Ryunosuke Yoshino; Takatsugu Hirokawa (J. Chem. Inf. Model., 2023)

Site Identification and Next Choice Protocol for Hit-to-Lead Optimization. - Genki Kudo; Takumi Hirao; Ryunosuke Yoshino; Yasuteru Shigeta; Takatsugu Hirokawa (J. Chem. Inf. Model., 2024)

CrypToth: Cryptic Pocket Detection through Mixed-Solvent Molecular Dynamics Simulations-Based Topological Data Analysis. - Jun Koseki; Chie Motono; Keisuke Yanagisawa; Genki Kudo; Ryunosuke Yoshino; Takatsugu Hirokawa; Kenichiro Imai (J. Chem. Inf. Model., 2025)

Construction of PROTAC-Mediated Ternary Complex Structure Distribution Profiles Using Extensive Conformational Search. - Genki Kudo; Takumi Hirao; Ryuhei Harada; Yasuteru Shigeta; Takatsugu Hirokawa; Ryunosuke Yoshino (J. Chem. Inf. Model., 2025)