Struct-NB: Predicting Protein-RNA Binding Sites Using Structural Features

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Article discussing predicting protein-RNA binding sites using structural features.

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18 p.: ill.

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Towfic, Fadi; Caragea, Cornelia; Gemperline, David; Dobbs, Drena & Honavar, Vasant 2008.

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The UNT College of Engineering promotes intellectual and scholarly pursuits in the areas of computer science and engineering, preparing innovative leaders in a variety of disciplines. The UNT College of Engineering encourages faculty and students to pursue interdisciplinary research among numerous subjects of study including databases, numerical analysis, game programming, and computer systems architecture.

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Article discussing predicting protein-RNA binding sites using structural features.

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18 p.: ill.

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Copyright © 2008. Reprinted with permission from Inderscience Publishers. International Journal of Data Mining and Bioinformatics, 4:1, pp. 21-43

Abstract: We explore whether protein-RNA interfaces differ from non-interfaces in terms of their structural features and whether structural features vary according to the type of the bound RNA (e.g., mRNA, siRNA, etc.), using a non-redundant dataset of 147 protein chains extracted from protein-RNA complexes in the Protein Data Bank. Furthermore, we use machine learning algorithms for training classifiers to predict protein-RNA interfaces using information derived from the sequence and structural features. We develop the Struct-NB classifier that takes into account structural information. We compare the performance of Naïve Bayes and Gaussian Naïve Bayes with that of Struct-NB classifiers on the 147 protein-RNA dataset using sequence and structural features respectively as input to the classifiers. The results of our experiments show that Struct-NB outperforms Naïve Bayes and Gaussian Naïve Bayes on the problem of predicting the protein-RNA binding interfaces in a protein sequence in terms of a range of standard measures for comparing the performance of classifiers.

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  • International Journal of Data Mining and Bioinformatics, 2008, Geneva: Inderscience Publishers

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  • Publication Title: International Journal of Data Mining and Bioinformatics
  • Volume: 4
  • Issue: 1
  • Page Start: 21
  • Page End: 43
  • Peer Reviewed: Yes

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UNT Scholarly Works

Materials from the UNT community's research, creative, and scholarly activities and UNT's Open Access Repository. Access to some items in this collection may be restricted.

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  • 2008

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  • Sept. 13, 2013, 2:58 p.m.

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  • March 27, 2014, 1:19 p.m.

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Towfic, Fadi; Caragea, Cornelia; Gemperline, David; Dobbs, Drena & Honavar, Vasant. Struct-NB: Predicting Protein-RNA Binding Sites Using Structural Features, article, 2008; [Geneva, Switzerland]. (digital.library.unt.edu/ark:/67531/metadc181676/: accessed August 19, 2017), University of North Texas Libraries, Digital Library, digital.library.unt.edu; crediting UNT College of Engineering.