中国物理B ›› 2020, Vol. 29 ›› Issue (10): 108708-.doi: 10.1088/1674-1056/abb7f3

所属专题: SPECIAL TOPIC — Modeling and simulations for the structures and functions of proteins and nucleic acids

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Huiwen Wang(王慧雯)1, Yunjie Zhao(赵蕴杰)1,†()   

  • 收稿日期:2020-04-30 修回日期:2020-07-07 接受日期:2020-09-14 出版日期:2020-10-05 发布日期:2020-10-05
  • 通讯作者: Yunjie Zhao(赵蕴杰)

Methods and applications of RNA contact prediction

Huiwen Wang(王慧雯) and Yunjie Zhao(赵蕴杰)†   

  1. 1 Institute of Biophysics and Department of Physics, Central China Normal University, Wuhan 430079, China
  • Received:2020-04-30 Revised:2020-07-07 Accepted:2020-09-14 Online:2020-10-05 Published:2020-10-05
  • Contact: Corresponding author. E-mail: yjzhaowh@mail.ccnu.edu.cn
  • About author:
    †Corresponding author. E-mail: yjzhaowh@mail.ccnu.edu.cn
    * Project supported by the National Natural Science Foundation of China (Grant No. 11704140) and Self-determined Research Funds of CCNU from the Colleges’ Basic Research and Operation of MOE (Grant No. CCNU20TS004).

Abstract:

The RNA tertiary structure is essential to understanding the function and biological processes. Unfortunately, it is still challenging to determine the large RNA structure from direct experimentation or computational modeling. One promising approach is first to predict the tertiary contacts and then use the contacts as constraints to model the structure. The RNA structure modeling depends on the contact prediction accuracy. Although many contact prediction methods have been developed in the protein field, there are only several contact prediction methods in the RNA field at present. Here, we first review the theoretical basis and test the performances of recent RNA contact prediction methods for tertiary structure and complex modeling problems. Then, we summarize the advantages and limitations of these RNA contact prediction methods. We suggest some future directions for this rapidly expanding field in the last.

Key words: RNA structure, contact prediction, direct coupling analysis, network, machine learning

中图分类号:  (RNA)

  • 87.14.gn
87.15.K- (Molecular interactions; membrane-protein interactions) 87.10.Ca (Analytical theories) 87.15.A- (Theory, modeling, and computer simulation)