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Title
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New tips for structure prediction by comparative modeling |
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Authors
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Anwar Rayan1, *
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Affiliation
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QRC-Qasemi Research Center,Al-Qasemi Academic College, P.O.B. 124, Baka El-Garbiah 30100, Israel | |
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a_rayan@qsm.ac.il; * Corresponding author | |
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Article Type
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Hypothesis | |
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Date
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received December 13, 2008; accepted December 29, 2008; published January 12, 2009 | |
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Abstract |
Comparative modelling is utilized to predict the 3-dimensional conformation of a given protein (target) based on its sequence alignment to experimentally determined protein structure (template). The use of such technique is already rewarding and increasingly widespread in biological research and drug development. The accuracy of the predictions as commonly accepted depends on the score of sequence identity of the target protein to the template. To assess the relationship between sequence identity and model quality, we carried out an analysis of a set of 4753 sequence and structure alignments. Throughout this research, the model accuracy was measured by root mean square deviations of Cα atoms of the target-template structures. Surprisingly, the results show that sequence identity of the target protein to the template is not a good descriptor to predict the accuracy of the 3-D structure model. However, in a large number of cases, comparative modelling with lower sequence identity of target to template proteins led to more accurate 3-D structure model. As a consequence of this study, we suggest new tips for improving the quality of comparative models, particularly for models whose target-template sequence identity is below 50%.
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Keywords |
comparative modelling; homology modelling; model refinement
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Citation |
Rayan, Bioinformation 3(6): 263-267 (2009) | |
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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
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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.
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