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Bioinformatics Advance Access published online on January 5, 2006
Bioinformatics, 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
Received November 28, 2005
Revised December 20, 2005
Accepted December 21, 2005

Applications note

OPM: orientations of proteins in membranes database

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

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

* To whom correspondence should be addressed.
Andrei L. Lomize, E-mail: almz{at}umich.edu


  Abstract

Summary: The OPM (Orientations of Proteins in Membranes) 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 membranes, 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.

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


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