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A novel method for protein 3d-structure similarity measure based on n-gram modeling

Deris, Safa'ai and Razmara, Jafar (2008) A novel method for protein 3d-structure similarity measure based on n-gram modeling. In: Proceeding of the 8th IEEE International Conference on Bioinformatics and Bioengineering. UNSPECIFIED, pp. 1-6.

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Official URL: http://dx.doi.org/10.1109/BIBE.2008.4696719

Abstract

The present paper describes a novel method for measuring structural similarity of proteins in three dimensions. The method gets its roots from computational linguistics and the related techniques for modeling protein structure in string form and pairwise comparison of protein sequences. The method uses n-gram based modeling techniques for capturing regularities in protein structure sequences and joints cross-entropy measures for comparing two protein sequences to do similarity test. In this way, the 3D- structure of protein is represented in string form and, then, a similarity test is performed over these sequences. To find an overlap between two protein structures in 3D-space, a superposition task is also applied. In order to confirm the validity of this method, some experiments were performed using a collection of the protein data sets on publicly available servers which showed that the method is efficient.

Item Type:Book Section
Additional Information:ISBN 978-142442845-8 ; IEEE International Conference on BioInformatics and BioEngineering, BIBE, 8-10 Oct. 2008, Athens
Uncontrolled Keywords:cross entropy; d-space; modeling technique; n-gram modeling; novel methods; pair-wise comparison; protein data; protein sequences, protein structures, structural similarity, structure similarity, three dimensions
Subjects:Q Science > QH Natural history > QH301 Biology
Divisions:Computer Science and Information System (Formerly known)
ID Code:11583
Deposited By: Nor Asmida Abdullah
Deposited On:28 Dec 2010 01:54
Last Modified:25 Feb 2011 09:26

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