Orientations of Proteins in Membranes database

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Orientations of Proteins in Membranes
Content
DescriptionThe database provides spatial arrangement of
PMID 16397007
Release date2005
Access
Data formatmodified PDB format
Websitehttp://opm.phar.umich.edu
Download URLOPM files
Tools
WebServer for calculating positions of proteins in membranes
Miscellaneous
LicenseCC-BY 3.0
Version2.0
Curation policyCurated

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

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
.

The database was widely used in experimental and theoretical studies of membrane-associated proteins.

lipidated amino acid residues) are missing in the experimental structures.[4] The database also does not include lower resolution structures with only main chain atoms provided by the Protein Data Bank. The calculated spatial arrangements of the lower resolution protein structures in the lipid bilayer can be found in other resources, such as PDBTM.[18]

References

  1. ^ ST NetWatch: Protein Databases Archived 2013-06-02 at the Wayback Machine review of OPM in Signal Transduction NetWatch list from Science
  2. PMID 16397007
    .
  3. PMID 16731967
    .
  4. ^
    PMID 17603894
    .
  5. PMID 21438609
    .
  6. PMID 21438606
    .
  7. PMID 15869384
    .
  8. PMID 10551860
    .
  9. PMID 11258945
    .
  10. PMID 11230696
    .
  11. PMID 16055150
    .
  12. S2CID 5704597
    .
  13. PMID 17237049
    .
  14. PMID 17056731
    .
  15. PMID 17367718
    .
  16. PMID 17028020
    .
  17. PMID 16641489
    .
  18. ^ "PDBTM: Protein Data Bank of Transmembrane Proteins". Archived from the original on 2013-12-25. Retrieved 2007-06-20.
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