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