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Chin. Phys. B, 2020, Vol. 29(7): 078702    DOI: 10.1088/1674-1056/ab889d
Special Issue: SPECIAL TOPIC — Modeling and simulations for the structures and functions of proteins and nucleic acids
SPECIAL TOPIC—Modeling and simulations for the structures and functions of proteins and nucleic acids Prev   Next  

Improving RNA secondary structure prediction using direct coupling analysis

Xiaoling He(何小玲), Jun Wang(王军), Jian Wang(王剑), Yi Xiao(肖奕)
School of Physics, Huazhong University of Science and Technology, Wuhan 430074, China
Abstract  Secondary structures of RNAs are the basis of understanding their tertiary structures and functions and so their predictions are widely needed due to increasing discovery of noncoding RNAs. In the last decades, a lot of methods have been proposed to predict RNA secondary structures but their accuracies encountered bottleneck. Here we present a method for RNA secondary structure prediction using direct coupling analysis and a remove-and-expand algorithm that shows better performance than four existing popular multiple-sequence methods. We further show that the results can also be used to improve the prediction accuracy of the single-sequence methods.
Keywords:  RNA secondary structure      structure prediction      direct coupling analysis  
Received:  23 March 2020      Revised:  08 April 2020      Published:  05 July 2020
PACS:  87.15.bd (Secondary structure)  
  87.14.gn (RNA)  
  87.15.A- (Theory, modeling, and computer simulation)  
Fund: Project supported by the National Natural Science Foundation of China (Grant No. 31570722).
Corresponding Authors:  Yi Xiao     E-mail:  yxiao@hust.edu.cn

Cite this article: 

Xiaoling He(何小玲), Jun Wang(王军), Jian Wang(王剑), Yi Xiao(肖奕) Improving RNA secondary structure prediction using direct coupling analysis 2020 Chin. Phys. B 29 078702

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