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)

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)

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)