Patent Document ID: 20030036093
Application ID: 09788006
Patent Flag: 0

Claim One:
1. A method of determining the existence and location of alpha helix regions of a polypeptide having an amino acid sequence, comprising: (a) defining a first segment of said amino acid sequence having a length, N, where N is an integer between 5 and about 15; (b) defining a further segment of the amino acid sequence, such further segment including a majority of the amino acid residues of the first segment, together with additional amino acid residue or residues adjacent to the first amino acid sequence; (c) performing atomistic modeling upon each segment to assay the free energy of each segment; (d) generating an ensemble of low energy conformations for each segment; (e) adjusting the ensemble for each segment to reflect a determination of entropic and free energy contributions for each segment; (f) modifying the ensemble for each segment to reflect the contributions to free energy accorded by at least one of cavity formation, solvation, and ionization; and (g) ascertaining the equilibrium probabilities for helical clusters to determine the probability of a residue or a segment being involved in an alpha helix region.