Patent ID: 7881918

Claim:
A profiler which spatially profiles a hydrophobicity distribution for a transmembrane protein based on a scaled hydrophobicity value, said profiler comprising a processor including: an identifier for identifying a residue external to a membrane and removing said residue to obtain a truncated structure comprising plural residue side-chains; a calculator which calculates plural residue centroids for said plural residue side-chains, calculates a distribution of said plural residue centroids, and obtains a geometric center for said distribution; and a profile generator which: selects a profiling geometry to approximate an external shape of the truncated structure within a lipid bilayer and generates a series of nested shapes consistent with the geometry; accumulates shifted and scaled values of residue hydrophobicity as a function of an increasing size of the nested shapes to generate an accumulated spatial distribution of residue hydrophobicity given by a function H (d) which is a sum of residue hydophobicity values within a cylinder of radius d; and spatially profiles the hydrophobicity distribution by calculating the values of H(d).