Orientations of Proteins in Membranes database

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Orientations of Proteins in Membranes
Content
Description The database provides spatial arrangement of proteins in the lipid bilayer
Data types
captured		 Protein structures from the PDB
Organisms All
Contact
Research center University of Michigan College of Pharmacy
Primary citation PMID 16397007
Release date 2005
Access
Data format modified PDB format
Website http://opm.phar.umich.edu
Download URL OPM files
Tools
Web Server for calculating positions of proteins in membranes
Miscellaneous
Version 2.0
Curation policy Curated

Orientations of Proteins in Membranes (OPM) database provides spatial positions of membrane protein structures with respect to the lipid bilayer.[1][2][3][4] Positions of the proteins are calculated using an implicit solvation model of the lipid bilayer.[5][6] The results of calculations were verified against experimental studies of spatial arrangement of transmembrane and peripheral proteins in membranes.[4][7][8][9][10][11][12]

Proteins structures are taken from the Protein Data Bank. OPM also provides structural classification of membrane-associated proteins into families and superfamilies, membrane topology, quaternary structure of proteins in membrane-bound state, and the type of a destination membrane for each protein. The coordinate files with calculated membrane boundaries are downloadable. The site allows visualization of protein structures with membrane boundary planes through Jmol, MDL Chime, WebMol and Discovery Studio.

The database was widely used in experimental and theoretical studies of membrane-associated proteins.[13][14][15][16][17] However, structures of many membrane-associated proteins are not included in the database if they can not be computationally predicted. This is the case when all membrane-anchoring parts of the proteins (amphiphilic alpha helices, exposed nonpolar residues, or lipidated amino acid residues) are missing in the experimental structures.[4]

References

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  1. ↑ ST NetWatch: Protein Databases review of OPM in Signal Transduction NetWatch list from Science
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