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Sequence-Based Prediction of RNA-Binding Residues in Proteins.


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.

SUBMITTER: Walia RR 

PROVIDER: S-EPMC5796408 | biostudies-literature | 2017

REPOSITORIES: biostudies-literature

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Sequence-Based Prediction of RNA-Binding Residues in Proteins.

Walia Rasna R RR   El-Manzalawy Yasser Y   Honavar Vasant G VG   Dobbs Drena D  

Methods in molecular biology (Clifton, N.J.) 20170101


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 ami  ...[more]

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