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RNA 3D Structure Analysis and Prediction pp 91–117Cite as

The RNA Folding Problems: Different Levels of sRNA Structure Prediction

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Part of the book series: Nucleic Acids and Molecular Biology ((NUCLEIC,volume 27))

Abstract

RNA 3D structure prediction is analogous to the protein folding problem, particularly the astronomical size of the conformational search space and the challenge of appropriately scoring native versus decoy alternatives. However, RNA presents important differences compared to proteins, notably the existence of a low-energy secondary structure intermediate on the pathway to tertiary folding. The availability of a secondary structure facilitates de novo prediction using assembly of fragments. RNA mutants and close homologs are readily predicted with high accuracy using homology modeling. Evolutionarily distant RNAs often require a combination of homology and de novo modeling approaches. The greatest challenges to RNA structure prediction are posed by multihelix loops, certain types of pseudoknots, and multidomain packing. There are also a variety of partial folding problems for RNA and opportunities for whole database structure prediction. Herein we describe a unified suite of programs called “RNA123” for the analysis and prediction of RNA structure.

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Acknowledgments

We thank Norm Watkins for managing NIH grant R44GM085889 and Astrid Tuin for preparing Fig. 6.8. This work was supported by NIH grants R01-GM073179 (P.I. John SantaLucia), U01-AI061192 (P.I. Philip Cunningham), and R44GM085889 (P.I. Norman E. Watkins, Jr., and Fredrick Sijenyi).

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Authors and Affiliations

  1. DNA Software, Inc., 334 E. Washington St., Ann Arbor, MI, 48104, USA

    Fredrick Sijenyi, Pirro Saro, Zheng Ouyang, Kelly Damm-Ganamet & John SantaLucia Jr.

  2. Department of Chemistry, Wayne State University, Detroit, MI, 48202, USA

    Marcus Wood, Jun Jiang & John SantaLucia Jr.

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  1. Fredrick Sijenyi
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  2. Pirro Saro
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  3. Zheng Ouyang
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  4. Kelly Damm-Ganamet
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  5. Marcus Wood
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  6. Jun Jiang
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  7. John SantaLucia Jr.
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Correspondence to John SantaLucia Jr. .

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Editors and Affiliations

  1. Dept. Chemistry, Bowling Green State University, Bowling Green, 43403, Ohio, USA

    Neocles Leontis

  2. Inst. Biologie Moleculaire, et Cellulaire, CNRS, rue Rene Descartes 15, Strasbourg CX, 67084, France

    Eric Westhof

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Sijenyi, F. et al. (2012). The RNA Folding Problems: Different Levels of sRNA Structure Prediction. In: Leontis, N., Westhof, E. (eds) RNA 3D Structure Analysis and Prediction. Nucleic Acids and Molecular Biology, vol 27. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-25740-7_6

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