Expediting protein structural analysis with an efficient kernel density estimation algorithm

Yen Jen Oyang, Tien-Hao Chang, Chien Yu Chen, Shien Ching Hwang

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 Citation (Scopus)

Abstract

We describe a kernel density estimation based mechanism aimed at expediting protein structural analysis. We have 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 α-hull algorithm from computer graphics, which features O(n2) time complexity, where n is the number of residues or atoms in the protein. A kernel density estimation based expediting mechanism with an average time complexity of O(nlogn) is proposed. We also report 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.

Original languageEnglish
Title of host publicationProceedings - IEEE 5th International Symposium on Multimedia Software Engineering, ISMSE 2003
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages297-304
Number of pages8
ISBN (Electronic)0769520316, 9780769520315
DOIs
Publication statusPublished - 2003 Jan 1
Event5th IEEE International Symposium on Multimedia Software Engineering, ISMSE 2003 - Taichung, Taiwan
Duration: 2003 Dec 102003 Dec 12

Publication series

NameProceedings - IEEE 5th International Symposium on Multimedia Software Engineering, ISMSE 2003

Other

Other5th IEEE International Symposium on Multimedia Software Engineering, ISMSE 2003
CountryTaiwan
CityTaichung
Period03-12-1003-12-12

All Science Journal Classification (ASJC) codes

  • Software

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  • Cite this

    Oyang, Y. J., Chang, T-H., Chen, C. Y., & Hwang, S. C. (2003). Expediting protein structural analysis with an efficient kernel density estimation algorithm. In Proceedings - IEEE 5th International Symposium on Multimedia Software Engineering, ISMSE 2003 (pp. 297-304). [1254455] (Proceedings - IEEE 5th International Symposium on Multimedia Software Engineering, ISMSE 2003). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/MMSE.2003.1254455