ProteoMix: an integrated and flexible system for interactively analyzing large numbers of protein sequences. - Eisuke Chikayama; Atsushi Kurotani; Yutaka Kuroda; Shigeyuki Yokoyama (Bioinform., 2004)

Identification of putative domain linkers by a neural network - application to a large sequence database. - Satoshi Miyazaki; Yutaka Kuroda; Shigeyuki Yokoyama (BMC Bioinform., 2006)

POODLE-L: a two-level SVM prediction system for reliably predicting long disordered regions. - Shuichi Hirose; Kana Shimizu; Satoru Kanai; Yutaka Kuroda; Tamotsu Noguchi (Bioinform., 2007)

Mathematical model for empirically optimizing large scale production of soluble protein domains. - Eisuke Chikayama; Atsushi Kurotani; Takanori Tanaka; Takashi Yabuki; Satoshi Miyazaki; Shigeyuki Yokoyama; Yutaka Kuroda (BMC Bioinform., 2010)

DROP: an SVM domain linker predictor trained with optimal features selected by random forest. - Teppei Ebina; Hiroyuki Toh; Yutaka Kuroda (Bioinform., 2011)

IS-Dom: a dataset of independent structural domains automatically delineated from protein structures. - Teppei Ebina; Yuki Umezawa; Yutaka Kuroda (J. Comput. Aided Mol. Des., 2013)

Correlations between predicted protein disorder and post-translational modifications in plants. - Atsushi Kurotani; Alexander A. Tokmakov; Yutaka Kuroda; Yasuo Fukami; Kazuo Shinozaki; Tetsuya Sakurai (Bioinform., 2014)

H-DROP: an SVM based helical domain linker predictor trained with features optimized by combining random forest and stepwise selection. - Teppei Ebina; Ryosuke Suzuki; Ryotaro Tsuji; Yutaka Kuroda (J. Comput. Aided Mol. Des., 2014)

Fast H-DROP: A thirty times accelerated version of H-DROP for interactive SVM-based prediction of helical domain linkers. - Tambi Richa; Soichiro Ide; Ryosuke Suzuki; Teppei Ebina; Yutaka Kuroda (J. Comput. Aided Mol. Des., 2017)

A Structural Model of Truncated Gaussia princeps Luciferase Elucidating the Crucial Catalytic Function of No.76 Arginine towards Coelenterazine Oxidation. - Nan Wu; Zhi-Chao Xu; Kai-Dong Du; Shen Huang; Naohiro Kobayashi; Yutaka Kuroda; Yan-Hong Bai (PLoS Comput. Biol., 2025)