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Beta-barrel outer membrane protein databases

Integral membrane proteins account for ∼20–30% of fully sequenced proteomes (Krogh et al., 2001). To date, two major structural architectures can be distinguished: the α-helical and the β-barrel membrane proteins. The former are located primarily in cell membranes of eukaryotic cells and bacterial inner membranes, while the latter are found exclusively in the outer membranes of Gram-negative bacteria and in the outer membranes of mitochondria and chloroplasts (Cavalier-Smith, 2000; Elofsson and von Heijne, 2007; Gray et al., 1999). The β-barrel outer membrane proteins (OMPs) are crucial for the life of bacteria, serving a variety of diverse roles, such as passive nutrient uptake and active transport of large molecules, protein secretion, enzymatic activity or adhesion to host cells (Schulz, 2003; Wimley, 2003; Schulz, 2000; Gromiha and Suwa, 2007). Source text: Tsirigos et al., 2011.

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TOPDOM
A collection of domains and sequence motifs located conservatively in one side of membranes either in transmembrane or globular proteins. TOPDOM was created by predicting the transmembrane status and topology of all protein sequence in UniProt database by the CCTOP algorithm and scanning by specific domain or motif detecting algorithms. The identified domain or motif was added to the database if it was uniformly annotated in the same side of the membrane of the various proteins in UniProt database.
OMPdb
A database of ß-barrel outer membrane proteins from Gram-negative bacteria. Information included in OMPdb consists of sequence data, as well as annotation for structural characteristics (such as the transmembrane segments), literature references and links to other public databases, features that are unique worldwide. OMPdb is useful for genome-wide analyses, comparative genomics as well as for providing training and test sets for predictive algorithms regarding transmembrane β-barrels.
TMPL / Transmembrane protein Models Positioned in the Lipid
Provides a database of transmembrane protein models positioned in the lipid bilayer. TMPL is a resource that includes atomistic and coarse-grained protein models oriented in the membrane by ANVIL algorithm, which has been designed to process both representations of protein structure. Users has the possibility to upload protein models and their membrane assignments to database. Most of the protein structures in TMPL come from external databases and were selected for containing the term “transmembrane” in either their keywords, title or description.
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