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A Protein Structure Comparison System based on PSAML  

Kim Jin-Hong (울산대학교 컴퓨터정보통신공학부)
Ahn Geon-Tae (울산대학교 컴퓨터정보통신공학부)
Byun Sang-Hee (울산대학교 컴퓨터정보통신공학부)
Lee Su-Hyun (창원대학교 컴퓨터공학과)
Lee Myung-Joon (울산대학교 컴퓨터정보통신공학부)
Publication Information
Journal of KIISE:Computing Practices and Letters / v.11, no.2, 2005 , pp. 133-148 More about this Journal
Abstract
Since understanding of similarities and differences among protein structures is very important for the study of the relationship between structure and function, many protein structure comparison systems have been developed. Hut, unfortunately, these systems introduce their own protein data derived from the PDB(Protein Data Bank), which are needed in their algorithms for comparing protein structures. In addition, according to the rapid increase in the size of PDB, these systems require much more computation to search for common substructures in their databases. In this paper, we introduce a protein structure comparison system named WS4E(A Web-Based Searching Substructures of Secondary Structure Elements) based on a PSAML database which stores PSAML documents using the eXist open XML DBMS. PSAML(Protein Structure Abstraction Markup Language) is an XML representation of protein data, describing a protein structure as the secondary structures of the protein and their relationships. Using the PSAML database, the WS4E provides web services searching for common substructures among proteins represented in PSAML. In addition, to reduce the number of candidate protein structures to be compared in the PSAML database, we used topology strings which contain the spatial information of secondary structures in a protein.
Keywords
PSAML; topology string; Protein Structure Comparison; XML; WS4E;
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