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Title |
A rapid protein structure alignment algorithm based on a text modeling technique |
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Authors |
Jafar Razmara1*, Safaai Deris1, Sepideh Parvizpour2 |
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Affiliation |
1Faculty of Computer Science and Information Systems, Universiti Teknologi Malaysia, Johor Bahru, Malaysia; 2Faculty of Bioscience and Bioengineering Universiti Teknologi Malaysia, Johor Bahru, Malaysia
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razmaraj@gmail.com; *Corresponding author
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Article Type |
Hypothesis
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Date |
Received May 08, 2011; Accepted May 09, 2011; Published July 19, 2011
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Abstract |
Structural alignment of proteins is widely used in various fields of structural biology. In order to further improve the quality of alignment, we describe an algorithm for structural alignment based on text modelling techniques. The technique firstly superimposes secondary structure elements of two proteins and then, models the 3D-structure of the protein in a sequence of alphabets. These sequences are utilized by a step-by-step sequence alignment procedure to align two protein structures. A benchmark test was organized on a set of 200 non-homologous proteins to evaluate the program and compare it to state of the art programs, e.g. CE, SAL, TM-align and 3D-BLAST. On average, the results of all-against-all structure comparison by the program have a competitive accuracy with CE and TM-align where the algorithm has a high running speed like 3D-BLAST.
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Keywords |
protein structure alignment; sequence alignment; text modeling.
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Citation |
Razmara et al.
Bioinformation 6(9): 344-347 (2011) |
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Edited by |
P Kangueane
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ISSN |
0973-2063
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Publisher |
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License |
This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License. |