An efficient mechanism for prediction of protein-ligand interactions based on analysis of protein tertiary substructures

Darby Tien Hau Chang, Chien Yu Chen, Yen Jen Oyang*, Hsueh Fen Juan, Hsuan Cheng Huang

*此作品的通信作者

研究成果: Conference contribution同行評審

4 引文 斯高帕斯(Scopus)

摘要

Analysis of protein-ligand interactions is a fundamental issue in drug design. As the detailed and accurate analysis of protein-ligand interactions involves calculation of binding free energy based on thermodynamics and even quantum mechanics, which is highly expensive in terms of computing time, conformational and structural analysis of proteins and ligands has been widely employed as a screening process in computer-aided drug design. In this paper, an efficient mechanism for identifying possible protein-ligand interactions based on analysis of protein tertiary substructures is proposed. In one experiment reported in this papert, the proposed prediction mechanism has been exploited to obtain some clues about a hypothesis that the biochemists have been speculating. The main distinction in the design of the prediction mechanism is the filtering process incorporated to expedite the analysis. The filtering process extracts the residues located in a cave of the protein tertiary structure for analysis and operates with O(nlogn) time complexity, where n is the number of residues in the protein. In comparison, the α-hull algorithm, which is a widely used algorithm in computer graphics for identifying those instances that are on the contour of a 3-dimensional object, features O(n2) time complexity. Experimental results show that the filtering process presented in this paper is able to speed up the analysis by a factor ranging from 3.11 to 9.79 times.

原文English
主出版物標題Proceedings - Fourth IEEE Symposium on Bioinformatics and Bioengineering, BIBE 2004
頁面427-433
頁數7
DOIs
出版狀態Published - 2004
事件Proceedings - Fourth IEEE Symposium on Bioinformatics and Bioengineering, BIBE 2004 - Taichung, Taiwan
持續時間: 19 5月 200421 5月 2004

出版系列

名字Proceedings - Fourth IEEE Symposium on Bioinformatics and Bioengineering, BIBE 2004

Conference

ConferenceProceedings - Fourth IEEE Symposium on Bioinformatics and Bioengineering, BIBE 2004
國家/地區Taiwan
城市Taichung
期間19/05/0421/05/04

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