The Application Of Distributed Parallel Processing And Complex Network In Protein Folding

Protein Folding is a chief problem in the Bioinformatics. It is how the amino acid sequence of a protein folds to three-dimensional structure and how to predict the three-dimensional structure of a protein from its one-dimensional sequence. Based on the Protein Folding thermodynamics theory, the research of Protein Folding expects to find the nature structure with minimal energy from the one-dimensional sequence.This thesis engages some researches in 3 aspects of Protein Folding. One is how to find a model that can better denote protein three-dimensional structure. Other is how to design algorithm to simulate the process of Protein Fold and to predict the three-dimensional structure. The third is how to improve the algorithm' s efficiency.The protein three-dimensional conformation model adopted by the thesis is HP trigonometry lattice model. This thesis discusses the model' s structure, the model' s denotation, the mode' s characteristic and how to describe it in programming. Based on this model, the thesis adopts a Parallel Genetic Algorithm for pattern searching in the tremendous conformation space, to simulate the process of Protein Fold and to find the three-dimensional structure with smallest free energy This thesis adopts coarse grain parallel Genetic Algorithm to improve computes efficiency and discusses the most key idea and important technique of this algorithm. Based on the data collected by computer, this thesis uses complex net model with two ways to establish a protein fold net and analyzes this complex net to get some rules. This thesis discusses this complex net' s structure and how to compute its attributes. Finally, conclusions of this thesis and suggestions for future research are given. This thesis has seven chapters.Chapter 1 introduces Human Genomic Project, Bioinformatics and main work done by the thesis.Chapter 2 introduces protein, protein fold problem, and modules ofthe system.Chapter 3 introduces the model of protein three-dimensional structure first, and then discusses how to use improving HP trigonometry lattice model to model the protein three-dimensional structure in this thesis in detail.Chapter 4 introduces the basic theory of distributed parallel computing.Chapter 5 introduces Parallel Genetic Algorithm' s basic theory first and then discusses how to use Parallel Genetic Algorithm to find the three-dimensional structure with smallest free energy in this thesis in detail.Chapter 6 introduces basic theory of complex network first. Then thi s thesis brings forward two ways to build the protein fold complex network and then builds two protein fold complex networks. At last, this thesis compares and analyzes the two protein fold complex networks.Chapter 7 summarizes this thesis, and suggestions for future research are given.This subject is supported by National Natural Science Foundation of China (subject NO, 60173046, 70371063).