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

The Membranome database was developed to assist analysis and computational modeling of singlepass (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 Methanocaldococ-cus 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 alpha-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.