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OPM DB specifications

Information


Unique identifier OMICS_26580
Name OPM DB
Alternative names Orientation of Proteins in Membranes database, OPM DB, OPM
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Not allowed
Maintained Yes

Publication for Orientation of Proteins in Membranes database

OPM DB citations

 (3)
library_books

Structural insight into the activation of a class B G protein coupled receptor by peptide hormones in live human cells

2017
eLife
PMCID: 5542768
PMID: 28771403
DOI: 10.7554/eLife.27711.025

[…] plex models obtained with crosslinking-restrained conformational modeling, and the system was suitably ionized to 0.15 M concentration of NaCl. Peptide-receptor complexes were pre-aligned in the OPM (Orientation of Proteins in Membranes) database (). CRF-CRF1R and dFXCRF(12-41)-CRF1R systems of 163467 and 165848 atoms, respectively, were created, which includes 38381 TIP3 waters and 312 POPC lipid […]

library_books

Modeling the Conformational Changes Underlying Channel Opening in CFTR

2013
PLoS One
PMCID: 3785483
PMID: 24086355
DOI: 10.1371/journal.pone.0074574

[…] 1 . A 120 Å×120 Å membrane patch consisting of 343 POPC residues was generated, into which the protein was inserted based on the calculated transmembrane position of the P-gp template recorded in the Orientation of Proteins in Membranes database . The system was then solvated and neutralized by the addition of TIP3P water molecules (a 3-site water model for which the CHARMM27 force field has been […]

library_books

Rapid membrane protein topology prediction

2011
Bioinformatics
PMCID: 3077071
PMID: 21493661
DOI: 10.1093/bioinformatics/btr119

[…] Today only 268 unique α-helical membrane protein structures are known according to the Orientation of Proteins in Membranes database (OPM, http://opm.phar.umich.edu/). The ‘topology’ of such proteins has proven to be a convenient concept. In essence, the topology specifies the number of […]

Citations

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OPM DB institution(s)
Computational Biophysics Laboratory (GRIB-IMIM), Universitat Pompeu Fabra, Barcelona Biomedical Research Park (PRBB), Barcelona, Spain; Institute of Neurosciences, National Research Council of Italy (IN-CNR), Padua, Italy; Acellera, Barcelona Biomedical Research Park (PRBB), Barcelona, Spain; Institució Catalana de Recerca i Estudis Avancats (ICREA), Barcelona, Spain
OPM DB funding source(s)
Supported by Acellera Ltd, MINECO (BIO2014-53095-P) and FEDER.

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