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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      Accepted manuscript online: 
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

[1] Li X, Bu D, Sun L, Wu Y, Fang S, Li H, Luo H, Luo C, Fang W, Chen R and Zhao Y 2017 Curr. Protoc Bioinf. 58 12.16.1
[2] Zhao Y, Li H, Fang S, Kang Y, Wu W, Hao Y, Li Z, Bu D, Sun N, Zhang M Q and Chen R 2016 Nucleic Acids Res. 44 D203
[3] Yang Y, Gu Q, Zhang B, Shi Y and Shao Z 2018 Chin. Phys. B 27 38701
[4] Shi Y, Wu Y, Wang F and Tan Z 2014 Chin. Phys. B 23 78701
[5] Bao L, Zhang X, Jin L and Tan Z 2016 Chin. Phys. B 25 18703
[6] Chang X, Xu L and Shi H 2015 Chin. Phys. B 24 128703
[7] Puton T, Kozlowski L P, Rother K M and Bujnicki J M 2013 Nucleic Acids Res. 41 4307
[8] Mathews D H, Turner D H and Watson R M 2016 Curr. Protoc Nucleic Acid Chem. 67 11.2.1
[9] Zuker M and Stiegler P 1981 Nucleic Acids Res. 9 133
[10] Zuker M 2003 Nucleic Acids Res. 31 3406
[11] Nussinov R, Pieczenik G, Griggs J R and Kleitman D J 1978 Siam J. Appl. Math. 35 68
[12] Bellaousov S, Reuter J S, Seetin M G and Mathews D H 2013 Nucleic Acids Res. 41 W471
[13] Lorenz R, Bernhart S H, Siederdissen C H Z, Tafer H, Flamm C, Stadler P F and Hofacker I L 2011 Algorithm Mol. Biol. 6 26
[14] Janssen S and Giegerich R 2015 Bioinformatics 31 423
[15] Doshi K J, Cannone J J, Cobaugh C W and Gutell R R 2004 Bmc Bioinf. 5 105
[16] Zhao Y, Wang J, Zeng C and Xiao Y 2018 Biophys. Rep. 4 123
[17] Tan Z, Fu Y H, Sharma G and Mathews D H 2017 Nucleic Acids Res. 45 11570
[18] Deigan K E, Li T W, Mathews D H and Weeks K M 2009 Proc. Natl. Acad. Sci. United States Am. 106 97
[19] Sukosd Z, Swenson M S, Kjems J and Heitsch C E 2013 Nucleic Acids Res. 41 2807
[20] De Leonardis E, Lutz B, Ratz S, Cocco S, Monasson R, Schug A and Weigt M 2015 Nucleic Acids Res. 43 10444
[21] Wang J, Mao K K, Zhao Y J, Zeng C, Xiang J J, Zhang Y and Xiao Y 2017 Nucleic Acids Res. 45 6299
[22] Morcos F, Pagnani A, Lunt B, Bertolino A, Marks D S, Sander C, Zecchina R, Onuchic J N, Hwa T and Weigt M 2011 Proc. Natl. Acad. Sci. USA 108 E1293
[23] de Juan D, Pazos F and Valencia A 2013 Nat Rev. Genet 14 249
[24] Morcos F, Hwa T, Onuchic J N and Weigt M 2014 Methods Molecular Biology 1137 55
[25] Zhao Y, Huang Y, Gong Z, Wang Y, Man J and Xiao Y 2012 Sci. Reports 2 734
[26] Wang J, Zhao Y, Zhu C and Xiao Y 2015 Nucleic Acids Res. 43 e63
[27] Wang J and Xiao Y 2017 Curr. Protoc Bioinf. 57 5 9 1
[28] Gouveia-Oliveira R and Pedersen A G 2007 Algorithms Mol. Biol. 2 12
[29] Fodor A A and Aldrich R W 2004 Proteins 56 211
[30] He X, Li S, Ou X, Wang J and Xiao Y 2019 Commun. Inf. Syst. 19 279
[31] Nawrocki E P, Burge S W, Bateman A, Daub J, Eberhardt R Y, Eddy S R, Floden E W, Gardner P P, Jones T A, Tate J and Finn R D 2015 Nucleic Acids Res. 43 D130
[32] Griffiths-Jones S, Bateman A, Marshall M, Khanna A and Eddy S R 2003 Nucleic Acids Res. 31 439
[33] Ekeberg M, Hartonen T and Aurell E 2014 J. Comput. Phys. 276 341
[34] Ekeberg M, Lovkvist C, Lan Y H, Weigt M and Aurell E 2013 Phys. Rev. E 87 012707
[35] Danaee P, Rouches M, Wiley M, Deng D, Huang L and Hendrix D 2018 Nucleic Acids Res. 46 5381
[36] Matthews B W 1975 Biochim. Biophysica Acta 405 442
[37] Parisien M, Cruz J A, Westhof E and Major F 2009 RNA 15 1875
[38] Yang H, Jossinet F, Leontis N, Chen L, Westbrook J, Berman H and Westhof E 2003 Nucleic Acids Res. 31 3450
[39] Lu X J, Bussemaker H J and Olson W K 2015 Nucleic Acids Res. 43 e142
[40] Zok T, Antczak M, Zurkowski M, Popenda M, Blazewicz J, Adamiak R W and Szachniuk M 2018 Nucleic Acids Res. 46 W30
[41] Hamada M, Sato K and Asai K 2011 Nucleic Acids Res. 39 393
[42] Tabei Y, Kiryu H, Kin T and Asai K 2008 Bmc Bioinf. 9 33
[43] Harmanci A O, Sharma G and Mathews D H 2011 Bmc Bioinf. 12 108
[44] Gruber A R, Bernhart S H and Lorenz R 2015 Methods Molecular Biology 1269 307
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