OPM: Orientations of Proteins in Membranes database

Mikhail A. Lomize; Andrei L. Lomize; Irina D. Pogozheva; Henry I. Mosberg

doi:10.1093/bioinformatics/btk023

Abstract

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. Availabililty: Contact: almz@umich.edu

Keywords

Membrane proteinTransmembrane proteinMembraneLipid bilayerPeripheral membrane proteinBilayerComputer scienceSortingChemistryIntegral membrane proteinDatabaseBioinformaticsBiophysicsBiologyBiochemistryAlgorithm

Affiliated Institutions

University of Michigan US

Related Publications

PRINCIPLES OF LYSOSOMAL MEMBRANE DIGESTION: Stimulation of Sphingolipid Degradation by Sphingolipid Activator Proteins and Anionic Lysosomal Lipids

Thomas Kolter , Konrad Sandhoff

Sphingolipids and glycosphingolipids are membrane components of eukaryotic cell surfaces. Their constitutive degradation takes place on the surface of intra-endosomal and intra-...

2005 Annual Review of Cell and Development... 458 citations

Molecular dynamics simulation of the gramicidin channel in a phospholipid bilayer.

Thomas B. Woolf , Benoı̂t Roux

A molecular dynamics simulation of the gramicidin A channel in an explicit dimyristoyl phosphatidylcholine bilayer was generated to study the details of lipid-protein interactio...

1994 Proceedings of the National Academy o... 283 citations

Transmembrane domain of influenza virus neuraminidase, a type II protein, possesses an apical sorting signal in polarized MDCK cells

Amitabha Kundu , Roy T. Avalos , Christopher M. Sanderson +1 more

The influenza virus neuraminidase (NA), a type II transmembrane protein, is directly transported to the apical plasma membrane in polarized MDCK cells. By using deletion mutants...

1996 Journal of Virology 196 citations

Determination of the Border between the Transmembrane and Cytoplasmic Domains of Human Integrin Subunits

Annika Armulik , IngMarie Nilsson , Gunnar von Heijne +1 more

In this study we have determined the position of the C-terminal end of the transmembrane domains of human integrin subunits (alpha2, alpha5, beta1, beta2) in microsomal membrane...

1999 Journal of Biological Chemistry 84 citations

Ectocytosis caused by sublytic autologous complement attack on human neutrophils. The sorting of endogenous plasma-membrane proteins and lipids into shed vesicles

Jürgen M. Stein , J. Paul Luzio

During sublytic complement attack on human neutrophils, plasma-membrane vesicles are shed from the cell surface as a cell-protection mechanism. By using surface-iodinated neutro...

1991 Biochemical Journal 226 citations

Publication Info

Year: 2006
Type: article
Volume: 22
Issue: 5
Pages: 623-625
Citations: 1165
Access: Closed

External Links

View on DOI.org

Social Impact

Altmetric

OPM: Orientations of Proteins in Membranes database

PlumX Metrics

Social media, news, blog, policy document mentions

Citation Metrics

1165

OpenAlex

Cite This

APA Style

                            
                                
                                    Mikhail A. Lomize, 
                                
                                    Andrei L. Lomize, 
                                
                                    Irina D. Pogozheva
                                
                                et al.
                            
                            (2006). 
                            OPM: Orientations of Proteins in Membranes database. 
                            Bioinformatics
                            , 22
                            (5)
                            , 623-625.
                            https://doi.org/10.1093/bioinformatics/btk023
                        

Identifiers

DOI: 10.1093/bioinformatics/btk023