Transmembrane proteins include membrane channels, pores, and receptors and, as such,
comprise an important part of the proteome, yet our knowledge about them is much less
complete than about soluble, globular proteins. An important aspect of transmembrane
protein structure is their exact position within the lipid bilayer, a feature hard
to investigate experimentally at the atomic level. Here we describe MemBlob, a novel
approach utilizing difference electron density maps obtained by cryo-EM studies of
transmembrane proteins. The idea behind is that the nonprotein part of such maps carries
information on the exact localization of the membrane mimetics used in the experiment
and can be used to extract the positional information of the protein within the membrane.
MemBlob uses a structural model of the protein and an experimental electron density
map to provide an estimation of the surface residues interacting with the membrane.