TMPDB: a database of experimentally-characterized transmembrane topologies.
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/.
Ikeda
Masami
M
Department of Electronic Information System Engineering, Faculty of Science and Technology, Hirosaki University, Hirosaki 036-8561, Japan.
Arai
Masafumi
M
Okuno
Toshikatsu
T
Shimizu
Toshio
T
D000818:Animals; D030562:Databases, Protein; D005057:Eukaryotic Cells; D008565:Membrane Proteins / Q000737:chemistry*; D011387:Prokaryotic Cells; D017433:Protein Structure, Secondary
D008565:Membrane Proteins