PPM

Positioning of proteins in flat and curved membranes. PPM 3.0 server features: - positioning of transmembrane and peripheral proteins and peptides in membranes and micelles - calculation of binding modes and membrane affinity of proteins taking into account the influence of hydrophobic matching and curvature stress - prediction of protein-induced membrane deformations - calculations in flat artificial and natural membranes - calculations in curved membranes with adjustable radii of curvature - calculations in spherical micelles of different sizes - positioning of proteins spanning two parallel membranes (e.g. outer and inner membranes of Gram-negative bacteria) - approximation of deformed membrane surfaces by several (up to four) flat surfaces - using polarity profiles along the membrane normal for the DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine) bilayer [PubMed] - using hydrophobic thicknesses (± 5Å) of artificial lipid bilayers (experimental values) and of different biological membranes (average values obtained from the large-scale analysis of transmembrane proteins from the OPM database)

homepage: https://opm.phar.umich.edu/ppm_server3

version	toolchain
3.0-20241222	GCC/13.3.0

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