Sequence-based prediction of RNA-binding residues in proteins

Rasna R. Walia, Yasser El-Manzalawy, Vasant G. Honavar, Drena Dobbs

Research output: Chapter in Book/Report/Conference proceedingChapter

1 Citation (Scopus)

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 timeconsuming. 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.

Original languageEnglish (US)
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Pages205-235
Number of pages31
DOIs
StatePublished - Jan 1 2017

Publication series

NameMethods in Molecular Biology
Volume1484
ISSN (Print)1064-3745

Fingerprint

RNA
Proteins
RNA-Binding Proteins
Binding Sites
Protein Binding
Software
Databases
Amino Acids

All Science Journal Classification (ASJC) codes

  • Molecular Biology
  • Genetics

Cite this

Walia, R. R., El-Manzalawy, Y., Honavar, V. G., & Dobbs, D. (2017). Sequence-based prediction of RNA-binding residues in proteins. In Methods in Molecular Biology (pp. 205-235). (Methods in Molecular Biology; Vol. 1484). Humana Press Inc.. https://doi.org/10.1007/978-1-4939-6406-2_15
Walia, Rasna R. ; El-Manzalawy, Yasser ; Honavar, Vasant G. ; Dobbs, Drena. / Sequence-based prediction of RNA-binding residues in proteins. Methods in Molecular Biology. Humana Press Inc., 2017. pp. 205-235 (Methods in Molecular Biology).
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Walia, RR, El-Manzalawy, Y, Honavar, VG & Dobbs, D 2017, Sequence-based prediction of RNA-binding residues in proteins. in Methods in Molecular Biology. Methods in Molecular Biology, vol. 1484, Humana Press Inc., pp. 205-235. https://doi.org/10.1007/978-1-4939-6406-2_15

Sequence-based prediction of RNA-binding residues in proteins. / Walia, Rasna R.; El-Manzalawy, Yasser; Honavar, Vasant G.; Dobbs, Drena.

Methods in Molecular Biology. Humana Press Inc., 2017. p. 205-235 (Methods in Molecular Biology; Vol. 1484).

Research output: Chapter in Book/Report/Conference proceedingChapter

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Walia RR, El-Manzalawy Y, Honavar VG, Dobbs D. Sequence-based prediction of RNA-binding residues in proteins. In Methods in Molecular Biology. Humana Press Inc. 2017. p. 205-235. (Methods in Molecular Biology). https://doi.org/10.1007/978-1-4939-6406-2_15