beta-Hairpins, alpha-helices, and the intermediates among the secondary structures in the energy landscape of a peptide from a distal beta-hairpin of SH3 domain. - Kazuyoshi Ikeda; Oxana V. Galzitskaya; Haruki Nakamura; Junichi Higo (J. Comput. Chem., 2003)

Assessing the druggability of protein-protein interactions by a supervised machine-learning method. - Nobuyoshi Sugaya; Kazuyoshi Ikeda (BMC Bioinform., 2009)

Kotai Antibody Builder: automated high-resolution structural modeling of antibodies. - Kazuo Yamashita; Kazuyoshi Ikeda; Karlou Mar Amada; Shide Liang; Yuko Tsuchiya; Haruki Nakamura; Hiroki Shirai; Daron M. Standley (Bioinform., 2014)

PoSSuM v.2.0: data update and a new function for investigating ligand analogs and target proteins of small-molecule drugs. - Jun-Ichi Ito; Kazuyoshi Ikeda; Kazunori D. Yamada; Kenji Mizuguchi; Kentaro Tomii (Nucleic Acids Res., 2015)

EzCatDB: the enzyme reaction database, 2015 update. - Nozomi Nagano; Naoko Nakayama; Kazuyoshi Ikeda; Masaru Fukuie; Kiyonobu Yokota; Takuo Doi; Tsuyoshi Kato; Kentaro Tomii (Nucleic Acids Res., 2015)

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)

PoSSuM v.3: A Major Expansion of the PoSSuM Database for Finding Similar Binding Sites of Proteins. - Yuko Tsuchiya; Tomoki Yonezawa; Yu Yamamori; Hiroko Inoura; Masanori Osawa; Kazuyoshi Ikeda; Kentaro Tomii (J. Chem. Inf. Model., 2023)

A new workflow for the effective curation of membrane permeability data from open ADME information. - Tsuyoshi Esaki; Tomoki Yonezawa; Kazuyoshi Ikeda (J. Cheminformatics, 2024)