Helix segment assignment in proteins using fuzzy logic

ABSTRACT

The automatic assignment of protein secondary structure from three dimensional coordinates is an essential step in the characterization of protein structure. Although, the recognition of secondary structures such as alpha-helices and beta-sheets seem straightforward, but there are many different definitions, each regarding different criteria. We have developed a new algorithm for protein helix assignment, by using fuzzy logic based on backbone torsion angles. In this method, each residue takes a number from 0 to 100 that indicates the helical membership degree of that residue. This method can be converted to a classical method whenever we assume that any residue with a membership degree greater than 83 is a helix. Comparison of the results with structures reported in protein data bank [PDB], dictionary of secondary structure 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 classical approaches used for protein structure comparisons and alignments