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A Comprehensive Review of Predicting Method of RNA Tertiary Structure

Received: 6 February 2021     Accepted: 1 March 2021     Published: 10 March 2021
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Abstract

In recent years, great progress has been made in the research of RNA function, and more and more RNA functions have been discovered. The function of RNA is highly dependent on its 3D structure, the RNA tertiary structure includes the RNA 3D structure and RNA tertiary interaction, so the RNA tertiary structure prediction has also attracted extensive attention. There are many RNA tertiary structure prediction algorithms. According to the traditional classification methods, the existing RNA tertiary structure prediction algorithms can be divided into two categories: the RNA tertiary structure prediction algorithm based on knowledge mining and the RNA tertiary structure prediction algorithm based on physics. On this basis, this paper further refines the RNA tertiary structure prediction algorithm based on physics in traditional classification, and proposes a new refinement classification method based on conformational sampling method, namely RNA tertiary structure prediction algorithm based on physical fragment assembly conformational sampling method and RNA tertiary structure prediction algorithm based on Stepwise ansatz conformational sampling method. We make a comparative analysis of RNA tertiary structure prediction algorithms, and put forward some suggestions for improving the energy function in the next step, in order to find an RNA tertiary structure prediction algorithm that can achieve atomic accuracy.

Published in Computational Biology and Bioinformatics (Volume 9, Issue 1)
DOI 10.11648/j.cbb.20210901.12
Page(s) 15-20
Creative Commons

This is an Open Access article, distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution and reproduction in any medium or format, provided the original work is properly cited.

Copyright

Copyright © The Author(s), 2021. Published by Science Publishing Group

Keywords

RNA Structure Prediction, Tertiary Structure, Conformational Sampling, Atomic Accuracy, Stepwise Ansatz

References
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[8] Leontis Neocles B, Stombaugh Jesse, Westhof Eric. The non-Watson-Crick base pairs and their associated isostericity matrices [J]. Nucleic acids research, 2002, 30 (16): 3497-531.
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  • APA Style

    Yurong Yang, Zhendong Liu. (2021). A Comprehensive Review of Predicting Method of RNA Tertiary Structure. Computational Biology and Bioinformatics, 9(1), 15-20. https://doi.org/10.11648/j.cbb.20210901.12

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    ACS Style

    Yurong Yang; Zhendong Liu. A Comprehensive Review of Predicting Method of RNA Tertiary Structure. Comput. Biol. Bioinform. 2021, 9(1), 15-20. doi: 10.11648/j.cbb.20210901.12

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    AMA Style

    Yurong Yang, Zhendong Liu. A Comprehensive Review of Predicting Method of RNA Tertiary Structure. Comput Biol Bioinform. 2021;9(1):15-20. doi: 10.11648/j.cbb.20210901.12

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  • @article{10.11648/j.cbb.20210901.12,
      author = {Yurong Yang and Zhendong Liu},
      title = {A Comprehensive Review of Predicting Method of RNA Tertiary Structure},
      journal = {Computational Biology and Bioinformatics},
      volume = {9},
      number = {1},
      pages = {15-20},
      doi = {10.11648/j.cbb.20210901.12},
      url = {https://doi.org/10.11648/j.cbb.20210901.12},
      eprint = {https://article.sciencepublishinggroup.com/pdf/10.11648.j.cbb.20210901.12},
      abstract = {In recent years, great progress has been made in the research of RNA function, and more and more RNA functions have been discovered. The function of RNA is highly dependent on its 3D structure, the RNA tertiary structure includes the RNA 3D structure and RNA tertiary interaction, so the RNA tertiary structure prediction has also attracted extensive attention. There are many RNA tertiary structure prediction algorithms. According to the traditional classification methods, the existing RNA tertiary structure prediction algorithms can be divided into two categories: the RNA tertiary structure prediction algorithm based on knowledge mining and the RNA tertiary structure prediction algorithm based on physics. On this basis, this paper further refines the RNA tertiary structure prediction algorithm based on physics in traditional classification, and proposes a new refinement classification method based on conformational sampling method, namely RNA tertiary structure prediction algorithm based on physical fragment assembly conformational sampling method and RNA tertiary structure prediction algorithm based on Stepwise ansatz conformational sampling method. We make a comparative analysis of RNA tertiary structure prediction algorithms, and put forward some suggestions for improving the energy function in the next step, in order to find an RNA tertiary structure prediction algorithm that can achieve atomic accuracy.},
     year = {2021}
    }
    

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  • TY  - JOUR
    T1  - A Comprehensive Review of Predicting Method of RNA Tertiary Structure
    AU  - Yurong Yang
    AU  - Zhendong Liu
    Y1  - 2021/03/10
    PY  - 2021
    N1  - https://doi.org/10.11648/j.cbb.20210901.12
    DO  - 10.11648/j.cbb.20210901.12
    T2  - Computational Biology and Bioinformatics
    JF  - Computational Biology and Bioinformatics
    JO  - Computational Biology and Bioinformatics
    SP  - 15
    EP  - 20
    PB  - Science Publishing Group
    SN  - 2330-8281
    UR  - https://doi.org/10.11648/j.cbb.20210901.12
    AB  - In recent years, great progress has been made in the research of RNA function, and more and more RNA functions have been discovered. The function of RNA is highly dependent on its 3D structure, the RNA tertiary structure includes the RNA 3D structure and RNA tertiary interaction, so the RNA tertiary structure prediction has also attracted extensive attention. There are many RNA tertiary structure prediction algorithms. According to the traditional classification methods, the existing RNA tertiary structure prediction algorithms can be divided into two categories: the RNA tertiary structure prediction algorithm based on knowledge mining and the RNA tertiary structure prediction algorithm based on physics. On this basis, this paper further refines the RNA tertiary structure prediction algorithm based on physics in traditional classification, and proposes a new refinement classification method based on conformational sampling method, namely RNA tertiary structure prediction algorithm based on physical fragment assembly conformational sampling method and RNA tertiary structure prediction algorithm based on Stepwise ansatz conformational sampling method. We make a comparative analysis of RNA tertiary structure prediction algorithms, and put forward some suggestions for improving the energy function in the next step, in order to find an RNA tertiary structure prediction algorithm that can achieve atomic accuracy.
    VL  - 9
    IS  - 1
    ER  - 

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Author Information
  • School of Computer Science and Technology, Shandong Jianzhu University, Jinan, China

  • School of Computer Science and Technology, Shandong Jianzhu University, Jinan, China

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