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Prediction Of Ligand Binding Sites In Rna Binding Protein Pockets Using Support Vector Machines
Author: Mittal,meetanshu,singh, Rahul, Raj Singh, Tiratha
Publisher: Internet Medical Publishing
7 pages
One time payment: €0.00
Required subscription: Free
Type of publication: Article
DOI: 10.3823/1020
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Description:

RNA binding proteins play a significant role in pattern regulation of gene expression during developmental phases. Therefore in order to facilitate our understanding of organism development there is a continuous need to develop an extensive a priori method for the prediction of RNA binding protein pockets.

We present here a SVM (Support Vector Machine) based approach for successful prediction of these pockets. The method employs two datasets: the protein sequences of the RNA binding protein pockets and the non RNA binding pro- tein pockets, both of which when combined to form the positive and negative datasets to be fed into the SVM model.

Before feeding the data to the SVM, both the datasets were crossed with several steps of sorting, which refined the selection process of obtaining ranked features of these datasets. Analysis was applied on 3 different featured datasets viz FPOCKET, Zernike and shell features. The results suggest that the top 10 features of shell are very important and play a pivotal role in the classification and prediction of ligand binding sites in RNA binding proteins. An accuracy of 89.3% was achieved when evaluated. This study demonstrates that it is possible to predict ligand binding sites in RNA binding protein pockets using its sequence.

 

About the publisher:

iMedPub Limited is a publishing house registered in UK, publishing medical books and journals since 2005. As an open service to doctors and biomedical researchers, it is driven by clinicians and researchers for themselves, while serving the interests of the general public. iMedPub disseminates research in a tiered system, beginning with our specialty books and journals and then working upwards. The grand vision of iMedPub is a world where all medical researchers and health professionals have an equal opportunity to seek, share and create knowledge. As we are a low cost academic publisher we offer the lowest article processing charges of all biomedical journals and publish books free of charges for authors.

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