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Bioinformatics Advance Access originally published online on November 11, 2004
Bioinformatics 2005 21(7):1276-1277; doi:10.1093/bioinformatics/bti121
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© The Author 2004. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

TMDET: web server for detecting transmembrane regions of proteins by using their 3D coordinates

Gábor E. Tusnády , Zsuzsanna Dosztányi and István Simon *

Institute of Enzymology, BRC, Hungarian Academy of Sciences H-1518 Budapest, PO Box 7, Hungary

*To whom correspondence should be addressed.

Summary: The structure of integral membrane proteins is determined in the absence of the lipid bilayer; consequently the membrane localization of the protein is usually not specified in the corresponding PDB file. Recently, we have developed a new method called TMDET which determines the most possible localization of the membrane relative to the protein structure, and gives the annotation of the membrane embedded parts of the sequence. The entire Protein Data Bank has been scanned by the new TMDET algorithm resulting in the database of structurally determined transmembrane proteins (PDB_TM). Here we present the web interface of the TMDET algorithm to allow scientists to determine the membrane localization of structural data prior to deposition or to analyze model structures.

Availability: The TMDET server is available for academic users on http://www.enzim.hu/TMDET

Contact: tusi{at}enzim.hu


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