Protein Structure Prediction Techniques Essay

This chapter presents an overview of protein structure prediction by representing some of the techniques. The structure prediction of protein has two main techniques. The secondary structure prediction and tertiary structure prediction methods are also discussed in this chapter.

2.1 OVERVIEW OF PROTEIN STRUCTURE PREDICTION TECHNIQUES Proteins perform many biological functions and represent the building blocks of organisms. Basically there are 20 types of amino acids in proteins consists of different chemical properties. A long chain of these amino acids forms the protein molecule with the neighbor through a covalent peptide bond. Proteins are also known as polypeptides. Protein folding is the collection of proteins into larger structures

The Secondary structure of protein consists of four structures such as alpha helix, beta sheet, coil and turn structure. Secondary structure prediction techniques are shown in fig 2.1

Statistical Methods

Chou-Fasman (CF) Method Chou et. al. (1974)., proposed the Chou-Fasman method is the one of the first method for the implementation of secondary structure prediction of protein. The method involves a matrix of two values: propensity values, a given amino acid will appear within the structure and frequency values, found in a hairpin turn for a provided amino acid. Taking these values into account the method then predicts regions of α-helices, regions of β-sheets, and positions where β-turns may appear. Chou P.Y. and Fasman G.D (1974)., is used to predict the Alpha-helices and beta-strands predicted by setting a cut for the total propensity for a slice of four residues. The residues values were classified into helix or strand breakers and formers. In formers the residues positively contribute to the formation of the structural element. Breakers are used to prevent or stop its