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Bioinformatics. 2005 Apr 1;21(7):1276-7. Epub 2004 Nov 11.

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

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1
Institute of Enzymology, BRC, Hungarian Academy of Sciences, H-1518 Budapest, PO Box 7, Hungary.

Abstract

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.

PMID:
15539454
DOI:
10.1093/bioinformatics/bti121
[Indexed for MEDLINE]
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