OPM provides spatial arrangements of membrane proteins with respect to the hydrocarbon core of the lipid bilayer. OPM includes all unique experimental structures of transmembrane proteins and some peripheral proteins and membrane-active peptides . Each protein is positioned in a lipid bilayer of adjustable thickness by minimizing its transfer energy from water to the membrane. OPM provides structural classification and sorting according to different criteria . The calculations are in agreement with experimental studies of 24 transmembrane and 39 peripheral peptides and proteins.
There are several thousand Protein Data Bank (PDB) entries with structures of transmembrane, integral monotopic and peripheral peptides and proteins. However, the exact orientations of these peptides and proteins in biological membranes is unknown. A computational approach for optimizing the spatial arrangement of protein structures in lipid bilayers has been developed and applied here to all unique structures of transmembrane proteins and a significant number of peripheral proteins from the PDB.
