Proteins in Membranes

We have developed a computational method for Positioning of Proteins in Membranes (PPM) implemented in a web server that calculates spatial positions of proteins relative to membrane boundaries by optimizing the free energy of protein transfer from water to the membrane environment (Fig.1). High computational efficiency of the PPM method allowed us to calculate the spatial arrangement in the lipid bilayer of integral and peripheral membrane proteins from the Protein Data Bank. The results are collected into the Orientation of Proteins in Membranes (OPM) database (Fig.2).