RNA structure prediction：Progress and perspective

doi:10.1088/1674-1056/23/7/078701

中国物理B ›› 2014, Vol. 23 ›› Issue (7): 78701-078701.doi: 10.1088/1674-1056/23/7/078701

所属专题： TOPICAL REVIEW — Statistical Physics and Complex Systems

• TOPICAL REVIEW—Statistical Physics and Complex Systems • 上一篇下一篇

RNA structure prediction：Progress and perspective

时亚洲, 吴园燕, 王凤华, 谭志杰

Department of Physics and Key Laboratory of Artificial Micro- and Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China

收稿日期:2014-02-17 修回日期:2014-04-15 出版日期:2014-07-15 发布日期:2014-07-15
基金资助:
Project supported by the National Natural Science Foundation of China (Grant Nos. 11074191, 11175132, and 11374234), the National Basic Research Program of China (Grant No. 2011CB933600), and the Program for New Century Excellent Talents of China (Grant No. NCET 08-0408).

RNA structure prediction：Progress and perspective

Shi Ya-Zhou (时亚洲), Wu Yuan-Yan (吴园燕), Wang Feng-Hua (王凤华), Tan Zhi-Jie (谭志杰)

Department of Physics and Key Laboratory of Artificial Micro- and Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China

Received:2014-02-17 Revised:2014-04-15 Online:2014-07-15 Published:2014-07-15
Contact: Tan Zhi-Jie E-mail:zjtan@whu.edu.cn
About author:87.14.gn; 87.15.bd; 87.15.bg; 87.15.Cc
Supported by:
Project supported by the National Natural Science Foundation of China (Grant Nos. 11074191, 11175132, and 11374234), the National Basic Research Program of China (Grant No. 2011CB933600), and the Program for New Century Excellent Talents of China (Grant No. NCET 08-0408).

摘要/Abstract

摘要： Many recent exciting discoveries have revealed the versatility of RNAs and their importance in a variety of cellular functions which are strongly coupled to RNA structures. To understand the functions of RNAs, some structure prediction models have been developed in recent years. In this review, the progress in computational models for RNA structure prediction is introduced and the distinguishing features of many outstanding algorithms are discussed, emphasizing three-dimensional (3D) structure prediction. A promising coarse-grained model for predicting RNA 3D structure, stability and salt effect is also introduced briefly. Finally, we discuss the major challenges in the RNA 3D structure modeling.

关键词: RNA structure prediction, secondary structure, three-dimensional (3D) structure, coarse-grained model

Abstract: Many recent exciting discoveries have revealed the versatility of RNAs and their importance in a variety of cellular functions which are strongly coupled to RNA structures. To understand the functions of RNAs, some structure prediction models have been developed in recent years. In this review, the progress in computational models for RNA structure prediction is introduced and the distinguishing features of many outstanding algorithms are discussed, emphasizing three-dimensional (3D) structure prediction. A promising coarse-grained model for predicting RNA 3D structure, stability and salt effect is also introduced briefly. Finally, we discuss the major challenges in the RNA 3D structure modeling.

Key words: RNA structure prediction, secondary structure, three-dimensional (3D) structure, coarse-grained model

中图分类号: (RNA)

87.14.gn

87.15.bd (Secondary structure) 87.15.bg (Tertiary structure) 87.15.Cc (Folding: thermodynamics, statistical mechanics, models, and pathways)

时亚洲, 吴园燕, 王凤华, 谭志杰. RNA structure prediction：Progress and perspective[J]. 中国物理B, 2014, 23(7): 78701-078701.

Shi Ya-Zhou (时亚洲), Wu Yuan-Yan (吴园燕), Wang Feng-Hua (王凤华), Tan Zhi-Jie (谭志杰). RNA structure prediction：Progress and perspective[J]. Chin. Phys. B, 2014, 23(7): 78701-078701.

参考文献 123

[1]	Gesteland R F, Cech T R and Atkins J F 2006 The RNA World (3rd edn.) (New York: Cold Spring Harbor Press)
[2]	Crick F 1970 Nature 227 561
[3]	Griffiths-Jones S, Moxon S, Marshall M, Khanna A, Eddy S R and Bateman A 2005 Nucleic Acids Res. 33 121
[4]	Doherty E A and Doudna J A 2001 Annu. Rev. Biophys. Biomol. Struct. 30 457
[5]	Hannon G J 2002 Nature 418 244
[6]	Chen J and Zhang W 2012 J. Chem. Phys. 137 225102
[7]	Edwards T E, Klein D J and Ferré-D'Amaré A R 2007 Curr. Opin. Struct. Biol. 17 273
[8]	Tinoco I and Bustamante C 1999 J. Mol. Biol. 293 271
[9]	Levitt M 1969 Nature 224 759
[10]	Michel F and Westhof E 1990 J. Mol. Biol. 216 585
[11]	Harris M E, Nolan J M, Malhotra A, Brown J W, Harvey S C and Pace N R 1994 EMBO J. 13 3953
[12]	Stagg S M, Mears J A and Harvey S C 2003 J. Mol. Biol. 328 49
[13]	Shapiro B A, Yingling Y G, Kasprzak W and Bindewald E 2007 Curr. Opin. Struct. Biol. 17 157
[14]	Laing C and Schlick T 2010 J. Phys. Condens. Matter. 22 283101
[15]	Mathews D H 2006 J. Mol. Biol. 359 526
[16]	Puton T, Kozlowski L P, Rother K M and Bujnicki J M 2013 Nucleic Acids Res. 41 4307
[17]	Mathews D H and Turner D H 2006 Curr. Opin. Struct. Biol. 16 270
[20]	Bernhart S H, Hofacker I L, Will S, Gruber A R and Stadler P F 2008 Bioinformatics 9 474
[21]	Knudsen B and Hein J 2003 Nucleic Acids Res. 31 3423
[22]	Sükösd Z, Knudsen B, Kjems J and Pedersen C N 2013 Bioinformatics 28 2691
[25]	Siebert S and Backofen R 2005 Bioinformatics 21 3352
[29]	Zuker M and Stiegler P 1981 Nucleic Acids Res. 9 133
[30]	Reuter J S and Mathews D H 2010 Bioinformatics 11 129
[31]	Hofacker I L and Stadler P F 2006 Bioinformatics 22 1172
[33]	Do C B, Woods D A and Batzoglou S 2006 Boinformatics 23 90
[34]	Ding Y and Lawrence C E 2003 Nucleic Acids Res. 31 7280
[35]	Giegerich R, Voss B and Rehmsmeier M 2004 Nucleic Acids Res. 32 4843
[38]	Geis M, Flamm C, Wolfinger M T, Tanzer A, Hofacker I L, Middendorf M, Mandl C, Stadler P F and Thurner C 2008 J. Mol. Biol. 379 160
[39]	Shapiro B A, Wu J C, Bengali D and Potts M J 2001 Bioinformatics 17 137
[41]	Rivas E and Eddy S R 1999 J. Mol. Biol. 285 2053
[42]	Ruan J, Stormo G D and Zhang W 2003 Bioinformatics 20 58
[43]	Ren J, Bastegari B, Condon A and Hoos H H 2005 RNA 11 1494
[46]	Reeder J and Giegerich R 2004 Bioinformatics 5 104
[18]	Madison J T, Everett G A and Kung H 1966 Science 153 531
[19]	Mathews D H and Turner D H 2002 J. Mol. Biol. 317 191
[23]	Harmanci A O Sharma G and Mathews D H 2011 Bioinformatics 12 108
[24]	Höchsmann M, Voss B and Giegerich R 2004 IEEEACM Trans. Comput. Biol. Bioinform. 1 53
[26]	Gardner P P and Giegerich R 2004 Bioinformatics 5 140
[27]	Tinoco I, Uhlenbeck O C and Levine M D 1971 Nature 230 362
[28]	Xia T, SantaLucia J, Burkand M E, Kierzek R, Schroeder S J, Jiao X, Cox C and Turner D H 1998 Biochemistry 37 14719
[32]	Zuker M 2000 Curr. Opin. Struct. Biol. 10 303
[36]	Zhang W and Chen S J 2002 Proc. Natl. Acad. Sci. USA 99 1931
[37]	Zhao P, Zhang W and Chen S J 2010 Biophys. J. 98 1617
[40]	Cao S and Chen S J 2006 Nucleic Acids Res. 34 2634
[44]	Chen X, He S M, Bu D, Zhang F, Wang Z, Chen R and Gao W 2008 Bioinformatics 24 1994
[45]	Xayaphoummine A, Bucher T and Isambert H 2005 Nucleic Acids Res. 33 605
[47]	Zhang J, Lin M, Chen R, Wang W and Liang J 2008 J. Chem. Phys. 128 125107
[48]	Chen S J 2008 Annu. Rev. Biophys. 37 197
[49]	Rother K, Rother M, Boniecki M, Puton T and Bujnicki J M 2011 J. Mol. Model 17 2325
[50]	Cruz J A, Blanchet M F, Boniecki M, Bujnicki J M, Chen S J, Cao S, Das R, Ding F, Dokholyan N V, Flores S C, Huang L, Lavender C A, Lisi V, Major F, Mikolajczak K, Patel D J, Philips A, Puton T, Santalucia J, Sijenyi F, Hermann T, Rother K, Rother M, Serganov A, Skorupski M, Soltysinski T, Sripakdeevong P, Tuszynska I, Weeks K M, Waldsich C, Wildauer M, Leontis N B and Westhof E 2012 RNA 18 610
[51]	Hajdin C E, Ding F, Dokholyan N V and Weeks K M 2010 RNA 16 1340
[52]	Massire C and Westhof E 1998 J. Mol. Graph. Model. 16 197
[53]	Zwieb C and Muller F 1997 Nucleic Acids Symp. Ser. 36 69
[54]	Martinez H M, Maizel J V and Shapiro B A 2008 J. Biomol. Struct. Dyn. 25 669
[55]	Jossinet F and Westhof E 2005 Bioinformatics 21 3320
[56]	Jossinet F, Ludwig T E and Westhof E 2010 Bioinformatics 26 2057
[59]	Rother M, Rother K, Puton T and Bujnicki J M 2011 Nucleic Acids Res. 39 4007
[60]	Flores S C and Altman R B 2010 RNA 16 1769
[61]	Zhao Y, Huang Y, Gong Z, Wang Y, Man J and Xiao Y 2012 Sci. Rep. 2 734
[63]	Popenda M, Szachniuk M, Antczak M, Purzycka K J, Lukasiak P, Bartol N, Blazewicz J and Adamiak R W 2012 Nucleic Acids Res. 40 e112
[68]	Parisien M and Major F 2008 Nature 452 51
[69]	Das R and Baker D 2007 Proc. Natl. Acad. Sci. USA 104 14664
[70]	Das R, Karanicolas J and Baker D 2010 Nat. Meth. 7 291
[71]	Bida J P and Maher L J 2012 RNA 18 385
[72]	Frellsen J, Moltke I, Thiim M, Mardia K V and Ferkinghoff-Borg J 2009 PloS Comput. Biol. 5 e1000406
[73]	Zhang J, Bian Y, Lin H and Wang W 2012 Phys. Rev. E 85 021909
[81]	Tan R K Z, Petrov A S and Harvey S C 2006 J. Chem. Theory Comput. 2 529
[82]	Jonikas M A, Radmer R J, Laederach A, Das R, Pearlman S, Herschlag D and Altman R B 2009 RNA 15 189
[83]	Ding F, Sharma S, Chalasani P, Demidov V V, Broude N E and Dokholyan N V 2008 RNA 14 1164
[84]	Sharma S, Ding F and Dokholyan N V 2008 Bioinformatics 24 1951
[85]	Cao S and Chen S J 2005 RNA 11 1884
[86]	Cao S and Chen S J 2011 J. Phys. Chem. B 115 4216
[87]	Xia Z, Gardner D P, Gutell R R and Ren P 2010 J. Phys. Chem. B 114 13497
[88]	Xia Z, Bell D R, Shi Y and Ren P 2013 J. Phys. Chem. B 117 3135
[89]	Pasquali S and Derreumaux P 2010 J. Phys. Chem. B 114 11957
[90]	Cragnolini T, Derreumaux P and Pasquali S 2013 J. Phys. Chem. B 117 8047
[57]	Zhang Y and Skolnick J 2013 BMC Biol. 11 44
[58]	Wu S and Zhang Y 2008 Bioinformatics 24 924
[62]	Zhao Y, Gong Z and Xiao Y 2011 J. Biomol. Struct. Dyn. 28 815
[64]	Tan Z J and Chen S J 2009 Methods Enzymol. 469 465
[65]	Case D A, Cheatham T E, Darden T, Gohlke H, Luo R, Merz K M, Onufriev A, Simmerling C, Wang B and Woods R J 2005 J. Comput. Chem. 26 1668
[66]	Gong Z, Zhao Y and Xiao Y 2010 J. Biomol. Struct. Dyn. 28 431
[67]	Brooks B R, Brooks C L, Mackerell A D, Nilsson L, Petrella R J, Roux B, Won Y, Archontis G, Bartels C, Boresch S, Caflisch A, Caves L, Cui Q, Dinner A R, Feig M, Fischer S, Gao J, Hodoscek M W, Kuczera K, Lazaridis T, Ma J, Ovchinnikov V, Paci E, Pastor R W, Post C B, Pu J Z, Schaefer M, Tidor B, Venable R M, Woodcock H L, Wu X, Yang W, York D M and Karplus M 2009 J. Comput. Chem. 30 1545
[74]	Zhang J, Zhang Y J and Wang W 2010 Chin. Phys. Lett. 27 118702
[75]	Zhang J, Dundas J, Lin M, Chen M, Wang W and Liang J 2009 RNA 15 2248
[76]	Laing C, Jung S, Kim N, Elmetwaly S, Zahran M and Schlick T 2013 PLoS ONE 8 e71947
[77]	Paliy M, Melnik R and Shapiro B A 2010 Phys. Biol. 7 036001
[78]	de Pablo J J 2011 Annu. Rev. Phys. Chem. 62 555
[79]	Leonarski F, Trovato F, Tozzini V, Les A and Trylska J 2013 J. Chem. Theory Comput. 9 4874
[80]	Malhotra A and Harvey S C 1994 J. Mol. Biol. 240 308
[91]	Denesyuk N and Thirumalai D 2013 J. Phys. Chem. B 117 4901
[92]	Hori N and Takada S 2012 J. Chem. Theory Comput. 8 3384
[93]	Woodson S A 2005 Curr. Opin. Chem. Biol. 9 104
[94]	Tan Z J and Chen S J 2011 Met. Ions Life Sci. 9 101
[95]	Wang F H, Wu Y Y and Tan Z J 2013 Biopolymers 99 370
[96]	Tan Z J and Chen S J 2008 Biophys. J. 95 738
[97]	Shi et al. 2014 (in submission)
[98]	Chauhan S and Woodson S A 2008 J. Am. Chem. Soc. 130 1296
[99]	Bailor M H, Mustoe A M, Brooks C L and Al-Hashimi H M 2011 Curr. Opin. Struct. Biol. 21 296
[100]	Wilkinson K A, Merino E J and Weeks K M 2006 Nat. Protoc. 1 1610
[101]	Parisien M and Major F 2012 J. Struct. Biol. 179 252
[102]	Das R, Kudaravalli M, Jonikas M, Laederach A, Fong R, Schwans J P, Baker D, Piccirilli J A, Altman R B and Herschlag D 2008 Proc. Natl. Acad. Sci. USA 105 4144
[103]	Seetin M J and Mathews D H 2011 J. Comput. Chem. 32 2232
[104]	Ding F, Lavender C A, Weeks K M and Dokholyan N V 2012 Nat. Methods 9 603
[105]	Pan J, Thirumalai D and Woodson S A 1997 J. Mol. Biol. 273 7
[106]	Hall K B 2012 Methods Mol. Biol. 875 67
[107]	Chen J, Gong S, Wang Y and Zhang W 2014 J. Chem. Phys. 140 025102
[108]	Zhang Y, Zhang J and Wang W 2011 J. Am. Chem. Soc. 133 6882
[109]	Draper D E 2013 Biopolymers 99 1105
[110]	Tan Z J and Chen S J 2005 J. Chem. Phys. 122 44903
[111]	Tan Z J and Chen S J 2006 Biophys. J. 90 1175
[112]	Tan Z J and Chen S J 2010 Biophys. J. 99 1565
[113]	Gong Z, Zhao Y, Chen C and Xiao Y 2011 J. Biomol. Struct. Dyn. 29 403
[114]	Ellis R J 2001 Curr. Opin. Struct. Biol. 11 114
[115]	Tan Z J and Chen S J 2012 Biophys. J. 103 827
[116]	Zhou H X 2008 Arch. Biochem. Biophys. 469 76
[117]	Draper D E 2008 Biophys J. 95 5489
[118]	Tan Z J and Chen S J 2011 Biophys. J. 101 176
[119]	Wu Y Y, Wang F H and Tan Z J 2013 Phys. Lett. A 377 1911
[120]	Hall K B 2002 Curr. Opin. Struct. Biol. 12 283
[121]	Wang Y, Chen X, Liu Z P, Huang Q, Wang Y, Xu D, Zhang X S, Chen R and Chen L 2013 Mol. Biosyst. 9 133
[122]	Wu T, Wang J, Liu C, Zhang Y, Shi B, Zhu X, Zhang Z, Skogerbo G, Chen L, Lu H, Zhao Y amd Chen R 2006 Nucleic Acids Res. 34 D150
[123]	Huang Y, Liu S, Guo D, Li L and Xiao Y 2013 Sci. Rep. 3 1887

RNA structure prediction：Progress and perspective

RNA structure prediction：Progress and perspective

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