TMPDB: a database of experimentally-characterized transmembrane topologies |
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Authors: | Ikeda Masami Arai Masafumi Okuno Toshikatsu Shimizu Toshio |
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Institution: | Department of Electronic Information System Engineering, Faculty of Science and Technology, Hirosaki University, Hirosaki 036-8561, Japan. |
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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 beta-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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