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RNA 3D Structure Analysis and Prediction pp 43–65Cite as

Why Can’t We Predict RNA Structure At Atomic Resolution?

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

Abstract

No existing algorithm can start with arbitrary RNA sequences and return the precise three-dimensional structures that ensure their biological function. This chapter outlines current algorithms for automated RNA structure prediction (including our own FARNA–FARFAR), highlights their successes, and dissects their limitations, using a tetraloop and the sarcin/ricin motif as examples. The barriers to future advances are considered in light of three particular challenges: improving computational sampling, reducing reliance on experimentally solved structures, and avoiding coarse-grained representations of atomic-level interactions. To help meet these challenges and better understand the current state of the field, we propose an ongoing community-wide CASP-style experiment for evaluating the performance of current structure prediction algorithms.

Sripakdeevong and Beauchamp are equally contributing authors.

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Note added in proof

Since the time of writing (2010), we have described a method called stepwise assembly that appears to resolve the conformational sampling bottleneck for small RNA loops (Sripakdeevong et al. 2011). Further, we and others have initiated RNA-Puzzles, a series of community-wide blind trials for RNA structure prediction (Cruz et al. 2012).

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Authors and Affiliations

  1. Biophysics Program, Stanford University, Stanford, CA, USA

    Parin Sripakdeevong, Kyle Beauchamp & Rhiju Das

  2. Biochemistry Department, Stanford University, Stanford, CA, USA

    Rhiju Das

Authors
  1. Parin Sripakdeevong
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  2. Kyle Beauchamp
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  3. Rhiju Das
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Correspondence to Rhiju Das .

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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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Sripakdeevong, P., Beauchamp, K., Das, R. (2012). Why Can’t We Predict RNA Structure At Atomic Resolution?. 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_4

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