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PDB_TM


NAR Molecular Biology Database Collection entry number 619
GÁbor E. TusnÁdy, Zsuzsanna DosztÁnyi and IstvÁn Simon
Institute of Enzymology, BRC, Hungarian Academy of Sciences, H-1113 Budapest, Karolina Út 29., HUNGARY
Contact tusi@enzim.hu

Database Description

Integral membrane proteins play important roles in living cells. Although these proteins are estimated to constitute around 25% of proteins at a genomic scale, the Protein Data Bank (PDB, http://www.rcsb.org/pdb) contains only a few hundred membrane proteins due to the difficulties with experimental techniques. The presence of transmembrane proteins in the structure data bank, however, is quite invisible, as the annotation of these entries is rather poor. Even if a protein is identified as a transmembrane one, the possible location of the lipid bilayer is not indicated in the PDB because these proteins are crystallized without their natural lipid bilayer.
In PDB_TM database we have collected all transmembrane proteins from PDB by using the TMDET (http://www.enzim.hu/TMDET) algorithm developed earlier. The possible localization of membrane plane is also determined together with the sequential localization of membraneaous part of the protein. These assigments are based on the TMDET algorithm as well, which uses structural information only to locate the most likely position of the lipid bilayer. By using TMDET algorithm, the PDB_TM database is automatically updated every week, keeping it synchronized with the latest PDB updates.

Acknowledgements

This work has been sponsored by grants BIO-0005/2001, OTKA T34131, D42207 and F043609. Zs.D. and G.E.T. were supported by the Bolyai Janos Scholarship.

Subcategory: Protein structure

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