Identification and Application of Functional Protein Substructure Base on Local Structure Comparison
Date Issued
2006
Date
2006
Author(s)
Sheu, Chi-Jun
DOI
zh-TW
Abstract
The functions of proteins are mainly affected by their structures. Therefore, the study of protein structures is helpful to realize the protein function. Protein structure comparison algorithm is one of the important tools in protein structure research.
In this thesis, we introduce a protein local structure comparison method. We try to find the common local substructures from proteins which have the same biochemical function. And then we can use those substructures to predict the protein function. In our algorithm has four main steps：1. pair-wise protein local structure comparison to find the common local substructures. 2. calculate the similarity between substructures. 3. cluster substructures by similarity 4. find the representative pattern.
In our experiment, we use the protein 3D viewer Jmol to show the location of patterns which we find and substrate. We can find out that patterns are near the substrates. Therefore, we can announce the patterns have some biochemical meaning. In addition, we compared our algorithm with 「Enzyme class prediction via mining conserved region in sequence and structure」algorithm（Lin ,2006）. We can find patterns from the EC numbers which it can’t find any patterns.
Subjects
蛋白質結構比對
局部結構比對
protein structure comparison
local structure comparison
Type
thesis
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