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Coarse-Grained Prediction of RNA Loop Structures

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  • Liang Liu
  • Shi-Jie Chen

Abstract

One of the key issues in the theoretical prediction of RNA folding is the prediction of loop structure from the sequence. RNA loop free energies are dependent on the loop sequence content. However, most current models account only for the loop length-dependence. The previously developed “Vfold” model (a coarse-grained RNA folding model) provides an effective method to generate the complete ensemble of coarse-grained RNA loop and junction conformations. However, due to the lack of sequence-dependent scoring parameters, the method is unable to identify the native and near-native structures from the sequence. In this study, using a previously developed iterative method for extracting the knowledge-based potential parameters from the known structures, we derive a set of dinucleotide-based statistical potentials for RNA loops and junctions. A unique advantage of the approach is its ability to go beyond the the (known) native structures by accounting for the full free energy landscape, including all the nonnative folds. The benchmark tests indicate that for given loop/junction sequences, the statistical potentials enable successful predictions for the coarse-grained 3D structures from the complete conformational ensemble generated by the Vfold model. The predicted coarse-grained structures can provide useful initial folds for further detailed structural refinement.

Suggested Citation

  • Liang Liu & Shi-Jie Chen, 2012. "Coarse-Grained Prediction of RNA Loop Structures," PLOS ONE, Public Library of Science, vol. 7(11), pages 1-15, November.
  • Handle: RePEc:plo:pone00:0048460
    DOI: 10.1371/journal.pone.0048460
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    References listed on IDEAS

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    1. Marc Parisien & François Major, 2008. "The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data," Nature, Nature, vol. 452(7183), pages 51-55, March.
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    Cited by:

    1. Jun Li & Wei Zhu & Jun Wang & Wenfei Li & Sheng Gong & Jian Zhang & Wei Wang, 2018. "RNA3DCNN: Local and global quality assessments of RNA 3D structures using 3D deep convolutional neural networks," PLOS Computational Biology, Public Library of Science, vol. 14(11), pages 1-18, November.
    2. Jun Li & Jian Zhang & Jun Wang & Wenfei Li & Wei Wang, 2016. "Structure Prediction of RNA Loops with a Probabilistic Approach," PLOS Computational Biology, Public Library of Science, vol. 12(8), pages 1-17, August.

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