A Comprehensive Review of Predicting Method of RNA Tertiary Structure

Yurong Yang; Zhendong Liu

doi:doi:10.11648/j.cbb.20210901.12

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A Comprehensive Review of Predicting Method of RNA Tertiary Structure

Yurong Yang, Zhendong Liu

Published in Computational Biology and Bioinformatics (Volume 9, Issue 1)

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), 2024. Published by Science Publishing Group

Keywords

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

References

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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

Yurong Yang

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

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

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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

Copy | Download

@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}
}

Copy | Download

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  -

Copy | Download