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Int. J. Mol. Sci. 2015, 16(11), 26303-26317; doi:10.3390/ijms161125952

Computational Prediction of RNA-Binding Proteins and Binding Sites

Center for Computational Biology, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
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Academic Editor: Tatyana Karabencheva-Christova
Received: 1 October 2015 / Revised: 20 October 2015 / Accepted: 23 October 2015 / Published: 3 November 2015
(This article belongs to the Collection Proteins and Protein-Ligand Interactions)
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Abstract

Proteins and RNA interaction have vital roles in many cellular processes such as protein synthesis, sequence encoding, RNA transfer, and gene regulation at the transcriptional and post-transcriptional levels. Approximately 6%–8% of all proteins are RNA-binding proteins (RBPs). Distinguishing these RBPs or their binding residues is a major aim of structural biology. Previously, a number of experimental methods were developed for the determination of protein–RNA interactions. However, these experimental methods are expensive, time-consuming, and labor-intensive. Alternatively, researchers have developed many computational approaches to predict RBPs and protein–RNA binding sites, by combining various machine learning methods and abundant sequence and/or structural features. There are three kinds of computational approaches, which are prediction from protein sequence, prediction from protein structure, and protein-RNA docking. In this paper, we review all existing studies of predictions of RNA-binding sites and RBPs and complexes, including data sets used in different approaches, sequence and structural features used in several predictors, prediction method classifications, performance comparisons, evaluation methods, and future directions. View Full-Text
Keywords: RNA-binding proteins (RBPs); RNA-binding site; bioinformatics; prediction; macromolecular docking RNA-binding proteins (RBPs); RNA-binding site; bioinformatics; prediction; macromolecular docking
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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Si, J.; Cui, J.; Cheng, J.; Wu, R. Computational Prediction of RNA-Binding Proteins and Binding Sites. Int. J. Mol. Sci. 2015, 16, 26303-26317.

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