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. 2017 Jan 4;45(D1):D250-D255.
doi: 10.1093/nar/gkw712. Epub 2016 Aug 10.

Membranome: a database for proteome-wide analysis of single-pass membrane proteins

Andrei L Lomize  1 , Mikhail A Lomize  2 , Shean R Krolicki  3 , Irina D Pogozheva  4
Affiliations

Membranome: a database for proteome-wide analysis of single-pass membrane proteins

Andrei L Lomize et al. Nucleic Acids Res. .

Abstract

The Membranome database was developed to assist analysis and computational modeling of single-pass (bitopic) transmembrane (TM) proteins and their complexes by providing structural information about these proteins on a genomic scale. The database currently collects data on >6000 bitopic proteins from Homo sapiens, Arabidopsis thaliana, Dictyostelium discoideum, Saccharomyces cerevisiae, Escherichia coli and Methanocaldococcus jannaschii It presents the following data: (i) hierarchical classification of bitopic proteins into 15 functional classes, 689 structural superfamilies and 1404 families; (ii) 446 complexes of bitopic proteins with known three-dimensional (3D) structures classified into 129 families; (iii) computationally generated three-dimensional models of TM α-helices positioned in membranes; (iv) amino acid sequences, domain architecture, functional annotation and available experimental structures of bitopic proteins; (v) TM topology and intracellular localization, (vi) physical interactions between proteins from the database along with links to other resources. The database is freely accessible at http://membranome.org There is a variety of options for browsing, sorting, searching and retrieval of the content, including downloadable coordinate files of TM domains with calculated membrane boundaries.

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Figures

Figure 1.
Figure 1.
Numbers of bitopic proteins from different organisms in the Membranome database (2016-02).
Figure 2.
Figure 2.
Comparison of bitopic protein sets in Membranome and UniProt databases. Percent of overlap between protein sets is indicated above each column.
Figure 3.
Figure 3.
Example of page for an individual bitopic protein from the Membranome database.
See this image and copyright information in PMC

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