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Nucleic Acids Research, 2003, Vol. 31, No. 1 406-409
© 2003 Oxford University Press

TMPDB: a database of experimentally-characterized transmembrane topologies

Masami Ikeda1,2, Masafumi Arai1, Toshikatsu Okuno2 and Toshio Shimizu*,1

1 Department of Electronic Information System Engineering, Faculty of Science and Technology, Hirosaki University, Hirosaki 036-8561, Japan 2 Science of Bioresources Program, The United Graduate School of Agricultural Sciences, Iwate University, Morioka 020-8550, Japan

*To whom correspondence should be addressed. Tel: +81 172393638; Fax: +81 172393638; Email: slsimi{at}si.hirosaki-u.ac.jp

ABSTRACT

TMPDB is a database of experimentally-characterized transmembrane (TM) topologies. TMPDB release 6.2 contains a total of 302 TM protein sequences, in which 276 are {alpha}-helical sequences, 17 ß-stranded, and 9 {alpha}-helical sequences with short pore-forming helices buried in the membrane. The TM topologies in TMPDB were determined experimentally by means of X-ray crystallography, NMR, gene fusion technique, substituted cysteine accessibility method, N-linked glycosylation experiment and other biochemical methods. TMPDB would be useful as a test and/or training dataset in improving the proposed TM topology prediction methods or developing novel methods with higher performance, and as a guide for both the bioinformaticians and biologists to better understand TM proteins. TMPDB and its subsets are freely available at the following web site: http://bioinfo.si.hirosaki-u.ac.jp/~TMPDB/.


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