The Method Of Protein Structure Alignment Based On Curve Match

Due to the close relationship with the study of protein function and evolution,protein structure alignment is a basic and important problem in bioinformatics. It hasimportant scientific and practical significances for enriching and developing oftheoretical foundations of protein structure, understanding the inherent implicationsamong protein structure, function and evolution, promoting the development of proteinstructure prediction and drug molecule design. Circling round the problem of proteinstructure alignment, the main contents of this paper are as follows:（1） On the basis of reading extensively domestic and foreign literature aboutprotein structure alignment, summarize existing methods of protein structure alignment.According to structure representation, these methods are classified and theirapplicability is summarized.（2） A New evaluation parameter of protein structure alignment proposed. Thisparameter comprehensively considers five aspects of the number of residue existed inalignment section of two structures, root mean squared distance, the number of sameresidues, the number of residue of the same secondary structure type and the gaprelative distance. The experiment test shows that this evaluation parameter improved isable to evaluate the quality of protein structure alignment effectively.（3） The protein structure alignment algorithm based on curve match is proposed.This method takes the curvature and the torsion of each referential position on curve asthe shape signature-twins to transform the three-dimensional structure curve to a one-dimensional twins-string. Thus, the protein structure alignment problem is simplified. Inorder to solve the problem of shape matching, a Binary Scoring Matrix of ShapeMatching (BSM) is proposed. According to the minimum continuous matchingfragments detected, two proteins compared are superimposed and the equivalentresidues are extracted by improved dynamic programming. In order to optimize thealignment, the mechanism of iterative optimization is employed in the method. Theresults of experiments verify the feasibility and correctness of this method.（4） Design of protein structure alignment system based on curve match. Thissystem can conveniently and effectively finish the process of protein structurealignment algorithm, which could be significant for the study of protein structure.