S. Shahriar Arab
Mehdi Sadeghi
Changiz Eslahchi
Hamid Pezeshk

The automatic assignment of the protein secondary structure from three dimensional coordinates is an essential step in the characterization of protein structure. There are several methods for assigning secondary structurefrom the three-dimensional structure based on different definitions. We developed a new algorithm for the protein secondary structure assignment, using fuzzy logic based on backbone angles. In this method, we assign a non negative number ranging from zero to one hundred to each residue to express the membership degree for being in a helix or betastrand. This method can be converted to the classical methods whenever we assume that any residue with membership degree greater than a selected cutoff be in a helix or beta strand structure. Comparison of the results with structures reported in PDB, DSSP and STRIDE for 4843 proteins show that our algorithm works as well as other classical methods. Also using fuzzy assignment in protein structural alignment, can lead us to an accurate results. FAssign is an online tool with a user-friendly interface, for assignment of proteins based on fuzzy assignment method(http://bioinf.cs.ipm.ir/softwares/fassign).

Protein structure, secondary structure assignment, fuzzy logic, protein alignment