The identification of transmembrane helices in transmembrane proteins is crucial,
not only to understand their mechanism of action, but also to develop new therapies.
While experimental data on the boundaries of membrane-embedded regions is sparse,
this information is present in cryo-electron microscopy (cryo-EM) density maps and
it has not been utilized yet for determining membrane regions. We developed a computational
pipeline, where the inputs of a cryo-EM map, the corresponding atomistic structure,
and the potential bilayer orientation determined by TMDET algorithm of a given protein
result in an output defining the residues assigned to the bulk water phase, lipid
interface, and the lipid hydrophobic core. Based on this method, we built a database
involving published cryo-EM protein structures and a server to be able to compute
this data for newly obtained structures.http://memblob.hegelab.org.Supplementary data
are available at Bioinformatics online.