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Species - Orientations of Proteins in Membranes (OPM) database

http://opm.phar.umich.edu/species.php

PDB ID or protein name. All proteins in OPM. Acanthoscurria gomesiana (Tarantula spider). Actinia fragacea (Strawberry anemone). Aedes aegypti (Yellowfever mosquito). Ambystoma tigrinum (Tiger salamander). Amycolatopsis orientalis (Nocardia orientalis). Androctonus australis (Sahara scorpion). Androctonus mauretanicus mauretanicus (Scorpion). Anguilla japonica (Japanese eel). Anopheles gambiae (African malaria mosquito). Anthopleura elegantissima (Sea anemone). Avian infectious bursal disease virus.

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Proteins - Orientations of Proteins in Membranes (OPM) database

http://opm.phar.umich.edu/proteins.php

PDB ID or protein name. All proteins in OPM. All proteins in OPM (3142 proteins). Num TM Sec. Structs. Hydrophobic Thickness or Depth (Å). Tilt Angle (°). Sensory rhodopsin, monomer. 319 ± 1.5. 13 ± 4. 318 ± 1.1. 0 ± 1. Sensory rhodopsin II, tetramer. 305 ± 1.1. 0 ± 0. 318 ± 1.4. 0 ± 1. 318 ± 1.3. 9 ± 2. Bacteriorhodopsin, K state, with lipids. 300 ± 0.6. 0 ± 0. Bacteriorhodopsin, trimer, complex with annular lipids. 298 ± 0.6. 0 ± 0. Sensory rhodopsin II, monomer. 303 ± 1.5. 15 ± 2. 296 ± 2.2. Squid rho...

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Families - Orientations of Proteins in Membranes (OPM) database

http://opm.phar.umich.edu/families.php

PDB ID or protein name. All proteins in OPM. Microbial and algal rhodopsins. 35 proteins) 3.E.1 (TCDB). G-protein coupled receptors, family A. 74 proteins) 9.A.14 (TCDB). GPCR Secretin (B) family. 4 proteins) 9.A.14 (TCDB). 6 proteins) 9.A.14 (TCDB). GPCR Metabotropic glutamate receptor (C) family. 2 proteins) 9.A.14 (TCDB). 1 protein) 1.C.113 (TCDB). Photosynthetic reaction centers from bacteria. 5 proteins) 3.E.2 (TCDB). 6 proteins) 5.B.4 (TCDB). 6 proteins) 5.B.4 (TCDB). 1 protein) 5.A.3 (TCDB). Trans...

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Classification - About OPM - Orientations of Proteins in Membranes (OPM) database

http://opm.phar.umich.edu/about.php?subject=classification

PDB ID or protein name. All proteins in OPM. Comparision with experimental data. Comparision with other computational methods. OPM consists of quaternary complexes (biological units) that are classified based on the structure of their main transmembrane or membrane-associated domain. The classification was built using SCOP. But it differs from both systems in certain aspects. There are four levels of hierarchy in the classification:. Evolutionarily related proteins with superimposable 3D structures.

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Localization (target membrane) - Orientations of Proteins in Membranes (OPM) database

http://opm.phar.umich.edu/localization.php

PDB ID or protein name. All proteins in OPM. Bacterial Gram-negative inner membrane. Bacterial Gram-negative outer membrane. Bacterial Gram-positive outer membrane. Bacterial Gram-positive plasma membrane. University of Michigan, Ann Arbor, MI 48109 USA.

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Methods - About OPM - Orientations of Proteins in Membranes (OPM) database

http://opm.phar.umich.edu/about.php?subject=methods

PDB ID or protein name. All proteins in OPM. Comparision with experimental data. Comparision with other computational methods. Each protein is considered as rigid body that freely floats in a hydrophobic slab of adjustable thickness. Orientation of the protein was determined by minimizing its transfer energy, ΔG. With respect to d. Variables in a coordinate system whose axis Z coincides with the bilayer normal:. Schematic representation of a transmembrane protein in a hydrophobic slab. Profiles of hydrog...

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Comparision with experimental data - About OPM - Orientations of Proteins in Membranes (OPM) database

http://opm.phar.umich.edu/about.php?subject=experiments

PDB ID or protein name. All proteins in OPM. Comparision with experimental data. Comparision with other computational methods. Comparison with experimental data. Comparison of computational results for transmembrane proteins with experimental studies of protein orientations in membranes. XSC, SL, CL, EM. Blaurock and Wilkins 1972; Barclay and Findlay 1984, Davison and Findlay 1986a,b; Hubbell et al. 2003, Krebs et al. 2003. SL, NMR, HM. Wegener et al. 2000. Photoreaction center from Rh. Spaeroides. Voss ...

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Membrane Protein Lipid Composition Atlas - Orientations of Proteins in Membranes (OPM) database

http://opm.phar.umich.edu/atlas.php

PDB ID or protein name. All proteins in OPM. Membrane Protein Lipid Composition Atlas. Bacterial Gram-negative inner membrane. Bacterial Gram-negative outer membrane. Bacterial Gram-positive outer membrane. Bacterial Gram-positive plasma membrane. Nat Rev Mol Cell Biol. 2008 Feb;9(2):112-24. Membrane lipids: where they are and how they behave. University of Michigan, Ann Arbor, MI 48109 USA.

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PPM Server - Orientations of Proteins in Membranes (OPM) database

http://opm.phar.umich.edu/server.php

PDB ID or protein name. All proteins in OPM. University of Michigan, Ann Arbor, MI 48109 USA.

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Features - About OPM - Orientations of Proteins in Membranes (OPM) database

http://opm.phar.umich.edu/about.php?subject=features

PDB ID or protein name. All proteins in OPM. Comparision with experimental data. Comparision with other computational methods. Of the proteins with calculated membrane boundaries are available for downloading separately for each protein or for a whole dataset. The coordinate files differ from original PDB entries:. The original PDB coordinates are transformed so that the calculated membrane normal coincides with the Z axis, the origin of coordinates corresponds to the middle of membrane.