NDLI: Augmenting SSEs with structural properties for rapid protein structure comparison

Content Provider	IEEE Xplore Digital Library
Author	Chern-Hooi Chionh Zhiyong Huang Kian-Lee Tan Zhen Yao
Copyright Year	2003
Description	Author affiliation: Dept. of Comput. Sci., Nat. Univ. of Singapore, Singapore (Chern-Hooi Chionh; Zhiyong Huang; Kian-Lee Tan; Zhen Yao)
Abstract	Comparing protein structures in three dimensions is a computationally expensive process that makes a full scan of a protein against a library of known protein structures impractical. To reduce the cost, we can use an approximation of the three dimensional structure that allows protein comparison to be performed quickly to filter away dissimilar proteins. In this paper we present a new algorithm, called SCALE, for protein structure comparison. In SCALE, a protein is represented as a sequence of secondary structure elements (SSEs) augmented with 3D structural properties such as the distances and angles between the SSEs. As such, the comparison between two proteins is reduced to a sequence alignment problem between their corresponding sequences of SSEs. The 3-D structural properties of the proteins contribute to the similarity score between the two sequences. We have implemented SCALE, and compared its performance against existing schemes. Our performance study shows that SCALE outperforms existing methods in terms of both efficiency and effectiveness (measured in terms of precision and recall).
Sponsorship	IEEE Comput. Soc. Inf. Technol. Res. Inst. at Wright State Univ. IEEE Neural Networks Soc
Starting Page	341
Ending Page	348
File Size	410653
Page Count	8
File Format	PDF
ISBN	0769519075
DOI	10.1109/BIBE.2003.1188972
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2003-03-12
Publisher Place	USA
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Proteins Bioinformatics Libraries Databases Computer science Genomics Drives Costs Filters Drugs
Content Type	Text
Resource Type	Article

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