PDB ID or protein name

Orientations of Proteins in Membranes (OPM) database

1v28
1v28 » Paralytic peptide 2

See all membrane protein images in OPM

OPM provides spatial arrangements of membrane proteins with respect to the hydrocarbon core of the lipid bilayer.

OPM includes all unique experimental structures of transmembrane proteins and some peripheral proteins and membrane-active peptides (Features).

Each protein is positioned in a lipid bilayer of adjustable thickness by minimizing its transfer energy from water to the membrane (Methods).

OPM provides structural classification and sorting according to different criteria (Classification).

Our calculations are in agreement with experimental studies of 24 transmembrane and 39 peripheral peptides and proteins (Comparison with Experiments).

Positions of all proteins were recalculated in June 2010 using a new implicit solvent model of the lipid bilayer, PPM 2.0 (see methods)

In citing the Orientations of Proteins in Membranes (OPM) database please refer to
Lomize MA, Lomize AL, Pogozheva ID, Mosberg HI (2006) OPM: Orientations of Proteins in Membranes database. Bioinformatics 22, 623-625. PDF PubMed

For an explanation of our method please refer to
Lomize AL, Pogozheva ID, Lomize MA, Mosberg HI (2006) Positioning of proteins in membranes: A computational approach. Protein Science 15, 1318-1333. PDF PubMed

For a new version of our method please refer to
Lomize AL, Pogozheva ID, Mosberg HI (2011) Anisotropic solvent model of the lipid bilayer. 2. Energetics of insertion of small molecules, peptides, and proteins in membranes. J Chem Inf Model 51, 930-946. PDF PDF (supplementary) PubMed

For more information on peripheral proteins please refer to
Lomize AL, Pogozheva ID, Lomize MA, Mosberg HI (2007) The role of hydrophobic interactions in positioning of peripheral proteins in membranes. BMC Struct Biol 7, 44. PDF PubMed
Questions
1. Calculate orientation for unreleased structure or membrane protein was not in OPM?

Please use our web server or we can process your coordinates through email (almz@umich.edu). All information is kept confidential. Orientation of membrane protein cannot be predicted if all its membrane-anchoring elements are missing or disordered.

2. Errors in orientation or experimental verification description?

Please contact us.

NSF OPM was funded by the National Science Foundation (NSF)
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