ProteMiner-SSM: A web server for efficient analysis of similar protein tertiary substructures

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

研究成果: Article同行評審

18 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, a web server called ProteMiner-SSM designed for efficient analysis of similar protein tertiary substructures is presented. In one experiment reported in this paper, the web server has been exploited to obtain some clues about a biochemical hypothesis. The main distinction in the software design of the web server is the filtering process incorporated to expedite the analysis. The filtering process extracts the residues located in the caves of the protein tertiary structure for analysis and operates with O(n log n) 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 three-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 3.15 to 9.37 times. The ProteMiner-SSM web server can be found at http://proteminer.csie.ntu.edu.tw/. There is a mirror site at http://p4.sbl.bc.sinica.edu.tw/proteminer/.

原文English
頁(從 - 到)W76-W82
期刊Nucleic acids research
32
發行號WEB SERVER ISS.
DOIs
出版狀態Published - 2004 七月 1

All Science Journal Classification (ASJC) codes

  • Genetics

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