OPM


21890895	OPM database and PPM web server: resources for positioning of proteins in membranes. [PMID: 21890895] Lomize MA, Pogozheva ID, Joo H, Mosberg HI, Lomize AL. Abstract The Orientations of Proteins in Membranes (OPM) database is a curated web resource that provides spatial positions of membrane-bound peptides and proteins of known three-dimensional structure in the lipid bilayer, together with their structural classification, topology and intracellular localization. OPM currently contains more than 1200 transmembrane and peripheral proteins and peptides from approximately 350 organisms that represent approximately 3800 Protein Data Bank entries. Proteins are classified into classes, superfamilies and families and assigned to 21 distinct membrane types. Spatial positions of proteins with respect to the lipid bilayer are optimized by the PPM 2.0 method that accounts for the hydrophobic, hydrogen bonding and electrostatic interactions of the proteins with the anisotropic water-lipid environment described by the dielectric constant and hydrogen-bonding profiles. The OPM database is freely accessible at http://opm.phar.umich.edu. Data can be sorted, searched or retrieved using the hierarchical classification, source organism, localization in different types of membranes. The database offers downloadable coordinates of proteins and peptides with membrane boundaries. A gallery of protein images and several visualization tools are provided. The database is supplemented by the PPM server (http://opm.phar.umich.edu/server.php) which can be used for calculating spatial positions in membranes of newly determined proteins structures or theoretical models. Nucleic Acids Res. 2012:40(Database issue) \| 1017 Citations (from Europe PMC, 2025-03-29)
16397007	OPM: orientations of proteins in membranes database. [PMID: 16397007] Lomize MA, Lomize AL, Pogozheva ID, Mosberg HI. Abstract SUMMARY: The Orientations of Proteins in Membranes (OPM) database provides a collection of transmembrane, monotopic and peripheral proteins from the Protein Data Bank whose spatial arrangements in the lipid bilayer have been calculated theoretically and compared with experimental data. The database allows analysis, sorting and searching of membrane proteins based on their structural classification, species, destination membrane, numbers of transmembrane segments and subunits, numbers of secondary structures and the calculated hydrophobic thickness or tilt angle with respect to the bilayer normal. All coordinate files with the calculated membrane boundaries are available for downloading. AVAILABILITY: http://opm.phar.umich.edu. Bioinformatics. 2006:22(5) \| 689 Citations (from Europe PMC, 2025-03-29)

OPM database and PPM web server: resources for positioning of proteins in membranes. [PMID: 21890895]

Lomize MA, Pogozheva ID, Joo H, Mosberg HI, Lomize AL.

The Orientations of Proteins in Membranes (OPM) database is a curated web resource that provides spatial positions of membrane-bound peptides and proteins of known three-dimensional structure in the lipid bilayer, together with their structural classification, topology and intracellular localization. OPM currently contains more than 1200 transmembrane and peripheral proteins and peptides from approximately 350 organisms that represent approximately 3800 Protein Data Bank entries. Proteins are classified into classes, superfamilies and families and assigned to 21 distinct membrane types. Spatial positions of proteins with respect to the lipid bilayer are optimized by the PPM 2.0 method that accounts for the hydrophobic, hydrogen bonding and electrostatic interactions of the proteins with the anisotropic water-lipid environment described by the dielectric constant and hydrogen-bonding profiles. The OPM database is freely accessible at http://opm.phar.umich.edu. Data can be sorted, searched or retrieved using the hierarchical classification, source organism, localization in different types of membranes. The database offers downloadable coordinates of proteins and peptides with membrane boundaries. A gallery of protein images and several visualization tools are provided. The database is supplemented by the PPM server (http://opm.phar.umich.edu/server.php) which can be used for calculating spatial positions in membranes of newly determined proteins structures or theoretical models.

Nucleic Acids Res. 2012:40(Database issue) | 1017 Citations (from Europe PMC, 2025-03-29)

OPM: orientations of proteins in membranes database. [PMID: 16397007]

Lomize MA, Lomize AL, Pogozheva ID, Mosberg HI.

Abstract

SUMMARY: The Orientations of Proteins in Membranes (OPM) database provides a collection of transmembrane, monotopic and peripheral proteins from the Protein Data Bank whose spatial arrangements in the lipid bilayer have been calculated theoretically and compared with experimental data. The database allows analysis, sorting and searching of membrane proteins based on their structural classification, species, destination membrane, numbers of transmembrane segments and subunits, numbers of secondary structures and the calculated hydrophobic thickness or tilt angle with respect to the bilayer normal. All coordinate files with the calculated membrane boundaries are available for downloading.
AVAILABILITY: http://opm.phar.umich.edu.

Bioinformatics. 2006:22(5) | 689 Citations (from Europe PMC, 2025-03-29)

URL:	http://opm.phar.umich.edu/
Full name:	Orientations of Proteins in Membranes Database
Description:	OPM provides spatial arrangements of membrane proteins with respect to the hydrocarbon core of the lipid bilayer.
Year founded:	2006
Last update:	2018-11-26
Version:
Accessibility:	Accessible
Country/Region:	United States

Data type:	Protein
Data object:	Animal Archaea Bacteria Fungi Plant Virus
Database category:	Structure
Major species:	Homo sapiens Mus musculus Zea mays Arabidopsis thaliana Oryza sativa Escherichia coli Saccharomyces cerevisiae
Keywords:	membrane protein

University/Institution:	University of Michigan
Address:	428 Church Street,Ann Arbor,MI 48109-1065 USA
City:	Ann Arbor
Province/State:	MI
Country/Region:	United States
Contact name (PI/Team):	Andrei L. Lomize
Contact email (PI/Helpdesk):	almz@umich.edu

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Database Commons a catalog of worldwide biological databases