Orientations of Proteins in Membranes (OPM) database provides spatial positions of

membrane protein Membrane proteins are common proteins that are part of, or interact with, biological membranes. Membrane proteins fall into several broad categories depending on their location. Integral membrane proteins are a permanent part of a cell membrane ...

structures with respect to the

lipid bilayer The lipid bilayer (or phospholipid bilayer) is a thin polar membrane made of two layers of lipid molecules. These membranes form a continuous barrier around all cell (biology), cells. The cell membranes of almost all organisms and many viruses a ...

. Positions of the proteins are calculated using an implicit solvation model of the lipid bilayer. The results of calculations were verified against experimental studies of spatial arrangement of

transmembrane A transmembrane protein is a type of integral membrane protein that spans the entirety of the cell membrane. Many transmembrane proteins function as gateways to permit the transport of specific substances across the membrane. They frequently u ...

and

peripheral A peripheral device, or simply peripheral, is an auxiliary hardware device that a computer uses to transfer information externally. A peripheral is a hardware component that is accessible to and controlled by a computer but is not a core compo ...

proteins in membranes. Proteins structures are taken from the

Protein Data Bank The Protein Data Bank (PDB) is a database for the three-dimensional structural data of large biological molecules such as proteins and nucleic acids, which is overseen by the Worldwide Protein Data Bank (wwPDB). This structural data is obtained a ...

. OPM also provides structural classification of membrane-associated proteins into families and superfamilies,

membrane topology Topology of a transmembrane protein refers to locations of N- and C-termini of membrane-spanning polypeptide chain with respect to the inner or outer sides of the biological membrane occupied by the protein. Several databases provide experimental ...

, quaternary structure of proteins in membrane-bound state, and the type of a destination

membrane A membrane is a selective barrier; it allows some things to pass through but stops others. Such things may be molecules, ions, or other small particles. Membranes can be generally classified into synthetic membranes and biological membranes. Bi ...

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 Jmol is computer software for molecular modelling of chemical structures in 3 dimensions. It is an open-source Java viewer for chemical structures in 3D. The name originated from ''Jva (the programming language) + olcules, and also the m ...

. The database was widely used in experimental and theoretical studies of membrane-associated proteins. However, structures of many membrane-associated proteins are not included in the database if their spatial arrangement in membrane can not be computationally predicted from the three-dimensional structure. This is the case when all membrane-anchoring parts of the proteins ( amphiphilic

alpha helices An alpha helix (or α-helix) is a sequence of amino acids in a protein that are twisted into a coil (a helix). The alpha helix is the most common structural arrangement in the secondary structure of proteins. It is also the most extreme type of l ...

, exposed nonpolar residues, or lipidated amino acid residues) are missing in the experimental structures. The database also does not include lower resolution structures with only main chain atoms provided by the

. The calculated spatial arrangements of the lower resolution protein structures in the lipid bilayer can be found in other resources, such as PDBTM.

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