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Protocols

OPM specifications

Information


Unique identifier OMICS_01612
Name OPM
Alternative name Orientations of Proteins in Membranes
Restrictions to use None
Database management system MySQL
Community driven No
Data access File download, Browse
User data submission Not allowed
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/Orientations_of_Proteins_in_Membranes_database

Maintainers


  • person_outline Andrei L. Lomize
  • person_outline Irina Pogozheva

Publications for Orientations of Proteins in Membranes

OPM citations

 (25)
library_books

X ray diffraction reveals the intrinsic difference in the physical properties of membrane and soluble proteins

2017
Sci Rep
PMCID: 5717104
PMID: 29208950
DOI: 10.1038/s41598-017-17216-1

[…] receptor and transporter proteins. Finally, two other subsets (embedded membrane proteins and proteins with extramembranous domains) were extracted based on spatial arrangements information from the ‘Orientations of Proteins in Membranes’ (OPM) database. Subsequent statistical analyses and charts rendering were conducted using Excel 2013 (Microsoft Corporation) and PRISM 7 (GraphPad Software, Inc) […]

call_split

A novel proton transfer mechanism in the SLC11 family of divalent metal ion transporters

2017
Sci Rep
PMCID: 5533754
PMID: 28754960
DOI: 10.1038/s41598-017-06446-y
call_split See protocol

[…] Coordinates of the inward-open ScaDMT were taken from the Orientations of Proteins in Membranes database (PDB ID: 4WGW). The co-crystallized manganese ion (Mn2+) was changed to cadmium (Cd2+) due to the lack of parameters for Mn2+ in the CHARMM36 force-fiel […]

library_books

Gene Duplication Leads to Altered Membrane Topology of a Cytochrome P450 Enzyme in Seed Plants

2017
Mol Biol Evol
PMCID: 5850782
PMID: 28505373
DOI: 10.1093/molbev/msx160

[…] segments of B. distachyon CYP73 proteins folded as pure alpha-helical structures. The full protein experimental structure of yeast CYP51 (ScErg11p) recently reported () was used as a control for OPM (Orientations of Proteins in Membranes) () database predictions. The membrane insertion/orientation parameters, including hydrophobic thickness, transfer energy and tilt angle determined by the PPM ser […]

library_books

Modeling Beta Traces for Beta Barrels from Cryo EM Density Maps

2017
Biomed Res Int
PMCID: 5259677
PMID: 28164115
DOI: 10.1155/2017/1793213

[…] simulated maps, fourteen large simulated maps, and eight experimental cryo-EM β-barrel maps. The proteins used in the simulated test set were collected from the β-barrel transmembrane superfamily of Orientations of Proteins in Membranes (OPM) database [] with less than 40% sequence similarity. The atomic structures of β-barrels were used to generate β-barrel density maps at 10 Å resolution using […]

call_split

Control of human VDAC 2 scaffold dynamics by interfacial tryptophans is position specific

2016
Biochim Biophys Acta
PMCID: 5091009
PMID: 27641490
DOI: 10.1016/j.bbamem.2016.09.011
call_split See protocol

[…] I-TASSER —modeled hVDAC-2 structure was used as the input file for all the simulations. The structure was first oriented in accordance to zebrafish VDAC-2 (PDB ID: 4BUM) template from Orientations of Proteins in Membranes (OPM) database , , using PyMOL v1.5.0.5 . The assembled hVDAC-2—micelle structure for simulations was generated using the Micelle Builder tool in the CHARMM-GUI w […]

library_books

Structural and Functional Effect of an Oscillating Electric Field on the Dopamine D3 Receptor: A Molecular Dynamics Simulation Study

2016
PLoS One
PMCID: 5104473
PMID: 27832207
DOI: 10.1371/journal.pone.0166412

[…] n the lipid bilayer [] 3 residues (29–30) and also missing atoms were added to the protein by Swiss-Pdb Viewer software.[]An appropriate orientation of the protein in the membrane was found by Server-Orientations of Proteins in Membranes (OPM) database.[] The 1-palmitoyl-2-oleoylsn-glycero-3- phosphatidylcholine (POPC) using the Membrane plugin distributed in VMD [] was used as a lipid bilayer whi […]

Citations

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OPM institution(s)
College of Pharmacy, University of Michigan, MI, USA; College of Literature, Science and the Arts, University of Michigan, MI, USA
OPM funding source(s)
This work was supported by National Institutes of Health (grant n°DA003910) and an Upjohn Research Award from the College of Pharmacy, University of Michigan.

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