Helix Segment Assignment in Proteins Using Fuzzy Logic

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The automatic assignment of protein secondary structure from three dimensional coordinates is an essentialstep in the characterization of protein structure.Although, the recognition of secondary structures suchas alpha-helices and beta-sheets seem straightforward, but there are many different definitions, eachregarding different criteria. We have developed a newalgorithm for protein helix assignment, by using fuzzylogic based on backbone torsion angles. In thismethod, each residue takes a number from 0 to 100that indicates the helical membership degree of thatresidue. This method can be converted to a classicalmethod whenever we assume that any residue with amembership degree greater than 83 is a helix.Comparison of the results with structures reported inprotein data bank (PDB), dictionary of secondarystructure of proteins (DSSP) and structure identification (STRIDE) for 324 proteins indicate that our algorithm works as well as DSSP showing 93% agreement.We believe that the fuzzy secondary structure assignment has more advantages than the other classicalapproaches used for protein structure comparisonsand alignments.