Paper Info
Title
Expediting Protein Structural Analysis With An Efficient Kernel Density Estimation Algorithm
Abstract
This paper describes a kernel density estimation based mechanism aimed at expediting protein structural analysis. This study, has been motivated by the observation that many protein structural analysis algorithms suffer high time complexity, while only the residues and atoms on the contour of a protein are essential for determining the functions of the protein and how it could interact with the other proteins. Accordingly, for some protein structural analysis problems, it is desirable to invoke a mechanism that can extract the residues and atoms on the contour of a protein in order to expedite the analysis process. The conventional approach to carry, out this task is to invoke the alpha-hull algorithm from computer graphics, which features O(n(2)) time complexity, where n is the number of residues or atoms in the protein. In this paper, a kernel density, estimation based expediting mechanism with an average time complexity of O(nlogn) is proposed. This paper also reports the experiment conducted to evaluate the effects of applying the proposed expediting mechanism to a real protein structural analysis problem. Experimental results reveal that a speedup of 4.8 to 10.3 times can be achieved with minimum impact on the analysis accuracy.
Year
DOI
Venue
2003
10.1109/MMSE.2003.1254455
IEEE FIFTH INTERNATIOANL SYMPOSIUM ON MULTIMEDIA SOFTWARE ENGINEERING, PROCEEDINGS
Keywords
Field
DocType
protein structural analysis, kernel density estimation, protein tertiary structure
Kernel (linear algebra),Algorithm design,Computer science,Expediting,Algorithm,Estimation theory,Time complexity,Computational complexity theory,Speedup,Kernel density estimation
Conference
Citations 
PageRank 
References 
2
0.54
3
Authors
4
Name
Order
Citations
PageRank
Yen-Jen Oyang142348.82
darby tienhau chang220.54
Chien-Yu Chen336729.24
Shien-ching Hwang414110.55