TMPDB: a database of experimentally-characterized transmembrane topologies
Open Access
- 1 January 2003
- journal article
- research article
- Published by Oxford University Press (OUP) in Nucleic Acids Research
- Vol. 31 (1) , 406-409
- https://doi.org/10.1093/nar/gkg020
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 α-helical sequences, 17 β-stranded, and 9 α-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/ .Keywords
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