Prediction of polypeptide secondary structures analysing the oscillation of the hydropathy profile

The hydropathy profile of a polypeptide can reflect periodicity tightly linked, in particular, with alpha-helix and beta-strand conformations. We have developed an algorithm to detect such periodicity to predict the secondary structure of proteins. The method uses profiles constructed with the weighted average of hydropathy along the primary structure of the polypeptide and does the analysis of the variation of the profile for looking for periodic oscillations, using a variation detecting algorithm, without the definition of an empirical threshold. The independence of the method from known structures makes it particularly reliable for analysing membrane proteins.