Algorithmic and Artificial Intelligence Methods for Protein Bioinformatics

Chapter 16

Fractal Related Methods for Predicting Protein Structure Classes and Functions

ZU-GUO YU, VO ANH, JIAN-YI YANG, and SHAO-MING ZHU

16.1 Introduction

The molecular function of a protein can be inferred from the protein's structure information [1]. It is well known that an amino acid sequence partially determines the eventual three-dimensional structure of a protein, and the similarity at the protein sequence level implies similarity of function [2, 3]. The prediction of protein structure and function from amino acid sequences is one of the most important and challenge problems in molecular biology.

Protein secondary structure, which is a summary of the general conformation and hydrogen bonding pattern of the amino acid backbone [4, 5], provides some knowledge to further simplify the complicated 3D structure prediction problem. Hence an intermediate but useful step is to predict the protein secondary structure. Since the 1970s, many methods have been developed for predicting protein secondary structure (see the more recent references cited in Ref. [6]).

Four main classes of protein structures, based on the types and arrangement of their secondary structural elements, were recognized [7]: (1) the helices, (2) the strands, and (3) those with a mixture of and shapes denoted ...