Sequence-Based Prediction of RNA-Binding Residues in Proteins

Date
2017-01-01
Authors
Walia, Rasna
Dobbs, Drena
EL-Manzalawy, Yasser
Honavar, Vasant
Dobbs, Drena
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Abstract

Identifying individual residues in the interfaces of protein–RNA complexes is important for understanding the molecular determinants of protein–RNA recognition and has many potential applications. Recent technical advances have led to several high-throughput experimental methods for identifying partners in protein–RNA complexes, but determining RNA-binding residues in proteins is still expensive and time-consuming. This chapter focuses on available computational methods for identifying which amino acids in an RNA-binding protein participate directly in contacting RNA. Step-by-step protocols for using three different web-based servers to predict RNA-binding residues are described. In addition, currently available web servers and software tools for predicting RNA-binding sites, as well as databases that contain valuable information about known protein–RNA complexes, RNA-binding motifs in proteins, and protein-binding recognition sites in RNA are provided. We emphasize sequence-based methods that can reliably identify interfacial residues without the requirement for structural information regarding either the RNA-binding protein or its RNA partner.

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<p>This is a chapter from<em> Prediction of Protein Secondary Structure </em>1484 (2017): 205, doi: <a href="http://dx.doi.org/10.1007/978-1-4939-6406-2_15" target="_blank">10.1007/978-1-4939-6406-2_15</a>. </p>
Keywords
Protein–RNA interfaces, Binding site prediction, Machine learning, RNA-binding proteins (RBPs), Ribonucleoprotein particles (RNPs), Homology-based prediction, RNABindRPlus, SNBRFinder, PS-PRIP, FastRNABindR
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