Transmembrane topology prediction methods: A re-assessment and improvement by a consensus method using a dataset of experimentally-characterized transmembrane topology . - Masami Ikeda; Masafumi Arai; Demelo Madrazo Lao; Toshio Shimizu (Silico Biol., 2001)

The presence of signal peptide significantly affects transmembrane topology prediction. - Demelo Madrazo Lao; Masafumi Arai; Masami Ikeda; Toshio Shimizu (Bioinform., 2002)

TMPDB: a database of experimentally-characterized transmembrane topologies. - Masami Ikeda; Masafumi Arai; Toshikatsu Okuno; Toshio Shimizu (Nucleic Acids Res., 2003)

ConPred II: a consensus prediction method for obtaining transmembrane topology models with high reliability. - Masafumi Arai; Hironori Mitsuke; Masami Ikeda; Jun-Xiong Xia; Takashi Kikuchi; Masanobu Satake; Toshio Shimizu (Nucleic Acids Res., 2004)

A proteome-wide analysis of domain architectures of prokaryotic single-spanning transmembrane proteins. - Masafumi Arai; Takafumi Fukushi; Masanobu Satake; Toshio Shimizu (Comput. Biol. Chem., 2005)