Paper Info
Title
ProteMiner-SSM: a web server for efficient analysis of similar protein tertiary substructures.
Abstract
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(nlogn) time complexity, where n is the number of residues in the protein. In comparison, the alpha-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(n(2)) 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/.
Year
DOI
Venue
2004
10.1093/nar/gkh425
NUCLEIC ACIDS RESEARCH
Keywords
Field
DocType
thermodynamics,proteins,computer graphic,structure analysis,kernel density estimate,protein structure,binding sites,integrins,drug design,time complexity,caspases,3 dimensional,ligands,software design,internet
Software design,Protein tertiary structure,Biology,Filter (signal processing),Computational science,Software,Bioinformatics,Genetics,Time complexity,Computer graphics,Web server,Speedup
Journal
Volume
Issue
ISSN
32
SUPnan
0305-1048
Citations 
PageRank 
References 
8
0.83
5
Authors
6
Name
Order
Citations
PageRank
Darby Tien-hao Chang122112.58
Chien-Yu Chen236729.24
Wen-Chin Chung3101.27
Yen-Jen Oyang442348.82
Hsueh-Fen Juan51219.52
Hsuan-Cheng Huang61349.60