PreDs: a server for predicting dsDNA-binding site on protein molecular surfaces. - Yuko Tsuchiya; Kengo Kinoshita; Haruki Nakamura (Bioinform., 2005)

PreBI: prediction of biological interfaces of proteins in crystals. - Yuko Tsuchiya; Kengo Kinoshita; Nobutoshi Ito; Haruki Nakamura (Nucleic Acids Res., 2006)

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)

Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures. - Akira R. Kinjo; Gert-Jan Bekker; Hirofumi Suzuki; Yuko Tsuchiya; Takeshi Kawabata; Yasuyo Ikegawa; Haruki Nakamura (Nucleic Acids Res., 2017)

Autoencoder-Based Detection of Dynamic Allostery Triggered by Ligand Binding Based on Molecular Dynamics. - Yuko Tsuchiya; Kei Taneishi; Yasushige Yonezawa (J. Chem. Inf. Model., 2019)

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)