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A novel text modeling approach for structural comparison and alignment of biomolecules

Razmara, Jafar and Deris, Safaai (2010) A novel text modeling approach for structural comparison and alignment of biomolecules. WSEAS Transactions on Computers, 9 (7). 675 - 685. ISSN 11092750

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Abstract

Within this paper, a novel strategy for structural alignment of proteins based on text modeling techniques is introduced. The method summarizes the protein secondary and tertiary structure in two textual sequences. The first sequence is used to initial superposition of secondary structure elements and the second sequence is employed to align the 3D-structure of two compared structures. The comparison technique used by the method has been inspired from computational linguistics for analysing and quantifying textual sequences. In this strategy, the cross-entropy measure over n-gram models is used to capture regularities between sequences of protein structures. The performance of the method is evaluated and compared with CE and SSM methods. The results of the experiments reported here provide evidence for the preference and applicability of the new approach in terms of efficiency and effectiveness.

Item Type:Article
Uncontrolled Keywords:cross-entropy, n-gram modeling, protein structure alignment
Subjects:Q Science > QA Mathematics > QA75 Electronic computers. Computer science
Divisions:Computer Science and Information System (Formerly known)
ID Code:22819
Deposited By: Narimah Nawil
Deposited On:02 Sep 2017 15:49
Last Modified:30 Nov 2018 14:22

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