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Nucleic Acids Research 2005 33(Database Issue):D275-D278; doi:10.1093/nar/gki002
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Nucleic Acids Research, 2005, Vol. 33, Database issue D275-D278
© 2005, the authors
Nucleic Acids Research, Vol. 33, Database issue © Oxford University Press 2005; all rights reserved

PDB_TM: selection and membrane localization of transmembrane proteins in the protein data bank

Gábor E. Tusnády, Zsuzsanna Dosztányi and István Simon*

Institute of Enzymology, BRC, Hungarian Academy of Sciences, H-1518 Budapest, P.O. Box 7, Hungary

* To whom correspondence should be addressed. Tel: +36 1 466 9276; Fax: +36 1 466 5465; Email: simon{at}enzim.hu

Received July 16, 2004; Revised and Accepted September 6, 2004

PDB_TM is a database for transmembrane proteins with known structures. It aims to collect all transmembrane proteins that are deposited in the protein structure database (PDB) and to determine their membrane-spanning regions. These assignments are based on the TMDET algorithm, which uses only structural information to locate the most likely position of the lipid bilayer and to distinguish between transmembrane and globular proteins. This algorithm was applied to all PDB entries and the results were collected in the PDB_TM database. By using TMDET algorithm, the PDB_TM database can be automatically updated every week, keeping it synchronized with the latest PDB updates. The PDB_TM database is available at http://www.enzim.hu/PDB_TM.

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