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Contribution to Book
Sequence-Based Prediction of RNA-Binding Residues in Proteins
Prediction of Protein Secondary Structure
  • Rasna R. Walia, United States Department of Agriculture
  • Yasser EL-Manzalawy, The Pennsylvania State University
  • Vasant G. Honavar, The Pennsylvania State University
  • Drena Dobbs, Iowa State University
Document Type
Book Chapter
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Published Version
Publication Date

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.


This is a chapter from Prediction of Protein Secondary Structure 1484 (2017): 205, doi: 10.1007/978-1-4939-6406-2_15.

Works produced by employees of the U.S. Government as part of their official duties are not copyrighted within the U.S. The content of this document is not copyrighted.
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Citation Information
Rasna R. Walia, Yasser EL-Manzalawy, Vasant G. Honavar and Drena Dobbs. "Sequence-Based Prediction of RNA-Binding Residues in Proteins" Prediction of Protein Secondary Structure Vol. 1484 (2017) p. 205 - 235
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