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RNA Chaperones pp 225-239 | Cite as

Disordered RNA-Binding Region Prediction with DisoRDPbind

  • Christopher J. Oldfield
  • Zhenling Peng
  • Lukasz KurganEmail author
Protocol
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Part of the Methods in Molecular Biology book series (MIMB, volume 2106)

Abstract

RNA chaperone activity is one of the many functions of intrinsically disordered regions (IDRs). IDRs function without the prerequisite of a stable structure. Instead, their functions arise from structural ensembles. A common theme in IDR function is molecular recognition; IDRs mediate interactions with other proteins, RNA, and DNA. Many computational methods are available to predict IDRs from protein sequence, but relatively few are available for predicting IDR functions. Available methods primarily focus on protein-protein interactions. DisoRDPbind was developed to predict several protein functions including interactions with RNA. This method is available as a user-friendly web interface, located at http://biomine.cs.vcu.edu/servers/DisoRDPbind/. The development and architecture of DisoRDPbind is briefly presented, and its accuracy relative to other RNA-binding residue predictors is discussed. We explain usage of the web interface in detail and provide an example of prediction results and interpretation. While DisoRDPbind does not identify RNA chaperones directly, we provide a case study of an RNA chaperone, HCV core protein, as an example of the method’s utility in the study of RNA chaperones.

Key words

Intrinsic disorder Protein-RNA interactions Intrinsically disordered regions Molecular recognition 

Notes

Acknowledgments

This research was supported in part by the Robert J. Mattauch Endowment funds and the National Science Foundation grant 1617369 to Lukasz Kurgan.

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2020

Authors and Affiliations

  • Christopher J. Oldfield
    • 1
  • Zhenling Peng
    • 2
  • Lukasz Kurgan
    • 1
    Email author
  1. 1.Department of Computer ScienceVirginia Commonwealth UniversityRichmondUSA
  2. 2.Center for Applied MathematicsTianjin UniversityTianjinPeople’s Republic of China

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