Predicting the Secondary Structure of Proteins by the Use of Hamming Distances and Alignment Scores

Abstract

Researchers are confident about the validity of the basic hypothesis that the secondary and tertiary structures of a protein are uniquely determined by its sequence of amino acids, that is its primary structure. In this article we use a database of 200 proteins. To find the secondary structure of a new protein, the first thirteen residues of this protein are taken as a substring. Then the conformations of the central amino acids of thirteen residue substrings of the proteins in the database, whose hamming distances are less than a given threshold or alignment scores exceed a given limit are collected in a basin. The commonest conformation in this basin is attached as the conformation of the central amino acid of the substring of the unknown protein. Using this technique, for MHsim threshold 3.0, a correct estimation rate of 53.4% is obtained with 4.74% indecisives and for MHsim threshold  5.0, the success was 56.93% with76.59% indecisives. When the half of the proteins, whose secondary structure estimations are higher, subjected to same calculation the following results are obtained; for MHsim threshold 3.0, correct estimation rate is 79.52% with 58.87% indecisives and for MHsim threshold 5.0, correct estimation rate is 65.52% with 5.02% indecisives. Average correct estimation rate for the alignment scores was %54.