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

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2010-01-01
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Towfic, Fadi
Caragea, Cornelia
Gemperline, David
Dobbs, Drena
Honavar, Vasant
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Dobbs, Drena
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Genetics, Development and Cell Biology

The Department of Genetics, Development, and Cell Biology seeks to teach subcellular and cellular processes, genome dynamics, cell structure and function, and molecular mechanisms of development, in so doing offering a Major in Biology and a Major in Genetics.

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The Department of Genetics, Development, and Cell Biology was founded in 2005.

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Bioinformatics and Computational Biology
The Bioinformatics and Computational Biology (BCB) Program at Iowa State University is an interdepartmental graduate major offering outstanding opportunities for graduate study toward the Ph.D. degree in Bioinformatics and Computational Biology. The BCB program involves more than 80 nationally and internationally known faculty—biologists, computer scientists, mathematicians, statisticians, and physicists—who participate in a wide range of collaborative projects.
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Computer ScienceGenetics, Development and Cell BiologyBioinformatics and Computational Biology
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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This is a manuscript of an article from International Journal of Data Mining and Bioinformatics 4 (2010): 21, doi: 10.1504/IJDMB.2010.030965. Posted with permission.

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Fri Jan 01 00:00:00 UTC 2010
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