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Bioinformatics Advance Access originally published online on January 5, 2006
Bioinformatics 2006 22(5):623-625; doi:10.1093/bioinformatics/btk023
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© The Author 2006. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

OPM: Orientations of Proteins in Membranes database

Mikhail A. Lomize 1, Andrei L. Lomize 2,*, Irina D. Pogozheva 2 and Henry I. Mosberg 2

1College of Literature, Science and the Arts, University of Michigan Ann Arbor, MI 48109-1065, USA
2College of Pharmacy, University of Michigan Ann Arbor, MI 48109-1065, USA

*To whom correspondence should be addressed.

Summary: The Orientations of Proteins in Membranes (OPM) database provides a collection of transmembrane, monotopic and peripheral proteins from the Protein Data Bank whose spatial arrangements in the lipid bilayer have been calculated theoretically and compared with experimental data. The database allows analysis, sorting and searching of membrane proteins based on their structural classification, species, destination membrane, numbers of transmembrane segments and subunits, numbers of secondary structures and the calculated hydrophobic thickness or tilt angle with respect to the bilayer normal. All coordinate files with the calculated membrane boundaries are available for downloading.

Availabililty: http://opm.phar.umich.edu

Contact: almz{at}umich.edu

Received on November 28, 2005; revised on December 20, 2005; accepted on December 21, 2005

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