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RNA Chaperones pp 225–239Cite as

Disordered RNA-Binding Region Prediction with DisoRDPbind

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Part of the book series: Methods in Molecular Biology ((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.

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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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Authors and Affiliations

  1. Department of Computer Science, Virginia Commonwealth University, Richmond, VA, USA

    Christopher J. Oldfield & Lukasz Kurgan

  2. Center for Applied Mathematics, Tianjin University, Tianjin, People’s Republic of China

    Zhenling Peng

Authors
  1. Christopher J. Oldfield
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  2. Zhenling Peng
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  3. Lukasz Kurgan
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Correspondence to Lukasz Kurgan .

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Editors and Affiliations

  1. Department of Pediatric Hematology, Oncology and Stem Cell Transplantation, University Hospital of Regensburg, Regensburg, Germany

    Tilman Heise

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Oldfield, C.J., Peng, Z., Kurgan, L. (2020). Disordered RNA-Binding Region Prediction with DisoRDPbind. In: Heise, T. (eds) RNA Chaperones. Methods in Molecular Biology, vol 2106. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-0231-7_14

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  • DOI: https://doi.org/10.1007/978-1-0716-0231-7_14

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