OPM database and PPM web server: resources for positioning of proteins in membranes

By Mikhail A. Lomize, Irina D. Pogozheva, Hyeon Joo, Henry I. Mosberg, Andrei L. Lomize. Nucleic Acids Res., 2011

1,959 citations recorded by the source corpus.

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.

Subfields: Molecular Biology

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Citations in the corpus

Transmembrane Membrane Readers form a Novel Class of Proteins That Include Peripheral Phosphoinositide Recognition Domains and Viral Spikes (2022, methodology): “0 [11,12], which predicts posi‐ tions of protein structures on fluid anisotropic solvent slabs that resemble membranes.”
A general-purpose protein design framework based on mining sequence–structure relationships in known protein structures (2018, background): “, those listed in the OPM database (71)] were excluded, 4) only domains ranging from 50 to 150 residues in lengths, consisting entirely of natural amino acids (including MSE, HSC, HSD, HSE, and HSP), and with no missing nonhydrogen backbone atoms were allowed, and 5) for X-ray PDB entries, only thos”
Database resources of the National Center for Biotechnology Information (2020, methodology): “…features include extended visualization of 2D interaction networks between proteins and ligands or other proteins, visualization of electrostatic potentials as computed by Delphi (21) and visualization of membrane bilayer location relative to membrane protein structures as provided by OPM (22).”
An Integrated Framework Advancing Membrane Protein Modeling and Design (2015, methodology): “These values can be computed from PPM [42] or TMDET [41], two servers that transform membrane protein structures into membrane coordinates with the membrane center at z = 0 and membrane normal along the z-axis.”
Protein Structure Prediction and Design in a Biologically Realistic Implicit Membrane. (2020, methodology): “Each protein is initialized in the orientation computed from theOrientations of Proteins inMembranes database (60), and the orientation is kept fixed during sequence search.”
MOLEonline: a web-based tool for analyzing channels, tunnels and pores (2018 update) (2018, methodology): “edu/) (21) or calculations by the MEMEMBED program (for structures without OPM membrane annotation) (22).”
Identification of an allosteric modulator of the serotonin transporter with novel mechanism of action. (2013, methodology): “Optimal positioning of the membrane was computed using the LeuT structure in the OPM database (Orientations of Proteins in Membranes; the PPM server) (Lomize et al., 2012).”
PDBTM: Protein Data Bank of transmembrane proteins after 8 years (2012, background): “In this, membrane proteins are classified using a simpler classification scheme than the one used by the OPM.”