AltPS: A Structural Alignment Tool for Protein Surfaces Using Similarity of Local Atomic Environments. - Minai, Ryoichi; Matsuo, Yo (Inf. Media Technol., 2010)

MMDB: Entrez's 3D structure database. - Marchler-Bauer, Aron; Addess, Kenneth J.; Chappey, Colombe; Geer, Lewis Y.; Madej, Thomas; Matsuo, Yo; Wang, Yanli; Bryant, Stephen H. (Nucleic Acids Res., 1999)

Prediction of protein secondary structure using the 3D-1D compatibility algorithm. - Ito, Masahiro; Matsuo, Yo; Nishikawa, Ken (Comput. Appl. Biosci., 1997)

An approach to systematic detection of protein structural motifs. - Matsuo, Yo; Kanehisa, Minoru (Comput. Appl. Biosci., 1993)