Chapter 5 - Protein Structure Prediction

Abstract

The prediction of protein secondary structures is an intermediate goal for determining its tertiary structure. The analysis on the performance of several secondary structure prediction methods in different structural classes shows that all the methods predict the secondary structure of all-α proteins more accurately than other classes. The successful prediction of the structural class and schemes developed for each class may help to improve the accuracy levels of secondary structure predictive schemes in globular proteins. Deciphering the native conformation of a protein from its amino acid sequence, termed, as “protein folding problem,” is one of the long-standing challenges in molecular and computational biology. Several methods have been proposed to predict the structural class, secondary structure content, location of secondary structures, and modeling tertiary structures. These methods have also been proposed for predicting the secondary structure content of a protein based on amino acid composition and residue-pair composition. The concept of “amino acid composition” plays a major role in predicting the structural class of globular proteins, and it is defined as the statistical preference of each of the amino acid residues occurring in protein molecules. Further these methods have been proposed to predict the secondary structures, and the success rate is limited with their own advantages and disadvantages.