Study on structural signature design and algorithms for index-based protein structure comparison
Date Issued
2007
Date
2007
Author(s)
Yang, Yi-Wei
DOI
zh-TW
Abstract
With the fast growth of determined protein structures in Protein Data Bank, to effectively analyze the relationship between protein structures has become a critical issue. Currently, protein structure comparison is the major approach to analyze protein structures and discover local functional regions. By evaluating similarity among protein structures, we can identify common substructures shared by the group of proteins. However, if we would like to mine local conserved regions among the group of protein structures, pair-wise protein structure comparison could be applied but it is still a time-consumed computational task because of the exponential growth of protein structures.
In this paper, we use sphere-based representation to describe protein local structure and apply indexing technique on protein structure to approach database search on Protein Data Bank for the purpose of protein structure mining. Our approach tries to filter out lots of non-similar protein structures to avoid unnecessary comparisons, and then compares multiple protein structures at the same time. While comparing with VAST and SSM in the capability of find protein structure under hierarchical functional classification of Enzyme Classification, our proposed approach has better performance in sensitivity and precision than VAST and SSM. Our experiment results reveal that our method could be a good approach to find protein structure with similar function. We provide the alternative for molecular biologists to search whole Protein Data Bank from the view of protein local structure.
Subjects
蛋白質結構搜尋
蛋白質結構比對
索引值設計
NRS
indexing
Protein structure
Type
thesis
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