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Special Issue:
SPECIAL TOPIC — Modeling and simulations for the structures and functions of proteins and nucleic acids
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| TOPICAL REVIEW—Modeling and simulations for the structures and functions of proteins and nucleic acids |
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Statistical potentials for 3D structure evaluation: From proteins to RNAs |
| Ya-Lan Tan(谭雅岚), Chen-Jie Feng(封晨洁), Xunxun Wang(王勋勋), Wenbing Zhang(张文炳)†, and Zhi-Jie Tan(谭志杰)‡ |
| Department of Physics and Key Laboratory of Artificial Micro & Nano-structures of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China |
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Abstract Structure evaluation is critical to in silico 3-dimensional structure predictions for biomacromolecules such as proteins and RNAs. For proteins, structure evaluation has been paid attention over three decades along with protein folding problem, and statistical potentials have been shown to be effective and efficient in protein structure prediction and evaluation. In recent two decades, RNA folding problem has attracted much attention and several statistical potentials have been developed for RNA structure evaluation, partially with the aid of the progress in protein structure prediction. In this review, we will firstly give a brief overview on the existing statistical potentials for protein structure evaluation. Afterwards, we will introduce the recently developed statistical potentials for RNA structure evaluation. Finally, we will emphasize the perspective on developing new statistical potentials for RNAs in the near future.
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Received: 27 June 2020
Revised: 02 September 2020
Accepted manuscript online: 14 October 2020
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| Fund: Project supported by the National Natural Science Foundation of China (Grant Nos. 11774272 and 11575128). The numerical calculations related to our work in this review were performed on the supercomputing system in the Supercomputing Center of Wuhan University. |
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Corresponding Authors:
†Corresponding author. E-mail: wbzhang@whu.edu.cn ‡Corresponding author. E-mail: zjtan@whu.edu.cn
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Cite this article:
Ya-Lan Tan(谭雅岚), Chen-Jie Feng(封晨洁), Xunxun Wang(王勋勋), Wenbing Zhang(张文炳), and Zhi-Jie Tan(谭志杰) Statistical potentials for 3D structure evaluation: From proteins to RNAs 2021 Chin. Phys. B 30 028705
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1 Gesteland R F, Cech T R and Atkins J F 2006 Q. Rev. Biol. 81 272
2 Dethoff E A, Chugh J, Mustoe A M and Alhashimi H M 2012 Nature 482 322
3 Guttman M and Rinn J L 2012 Nature 482 339
4 Doherty E A and Doudna J A 2001 Annu. Rev. Biophys. Biomol. Struct. 30 457
5 Edwards T E, Klein D J and Ferré-D'Amaré A R 2007 Curr. Opin. Struct. Biol. 17 273
6 Aviv T, Amborski A N, Zhao X S, Kwan J J, Johnson P E, Sicheri F and Donaldson L W 2006 J. Mol. Biol. 356 274
7 Baird N J, Ludtke S J, Khant H, Chiu W, Pan T and Sosnick T R 2010 J. Am. Chem. Soc. 132 16352
8 Rose P W, Prli\'c A, Altunkaya A, Bi C, Bradley A R, Christie C H, Costanzo L D, Duarte J M, Dutta S, Feng Z, Green R K, Goodsell D S, Hudson B, Kalro T, Lowe R, Peisach E, Randle C, Rose A S, Shao C, Tao Y P, Valasatava Y, Voigt M,Westbrook J D,Woo J, Yang H, Young J Y, Zardecki C, Berman H M and Burley S K 2017 Nucleic Acids Res. 45 D271
9 Miao Z, Adamiak R W, Antczak M, et al.2017 RNA 23 655
10 Sun L Z, Zhang D and Chen S J 2017 Annu. Rev. Biophys. 46 227
11 Schlick T and Pyle A M 2017 Biophys. J. 113 225
12 Shi Y Z, Wu Y Y, Wang F H and Tan Z J 2014 Chin. Phys. B 23 078701
13 Ding F, Sharma S, Chalasani P, Demidov V V, Broude N E and Dokholyan N V 2008 RNA 14 1164
14 Parisien M and Major F 2008 Nature 452 51
15 Jossinet F, Ludwig T E and Westhof E 2010 Bioinformatics 26 2057
16 Das R, Karanicolas J and Baker D 2010 Nat. Methods 7 291
17 Cao S and Chen S 2011 J. Phys. Chem. B 115 4216
18 Rother M, Rother K, Puton T and Bujnicki J M 2011 Nucleic Acids Res. 39 4007
19 Zhao Y, Huang Y, Gong Z, Wang Y, Man J and Xiao Y 2012 Sci. Rep. 2 734
20 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
21 Zhang J, Bian Y, Lin H and Wang W 2012 Phys. Rev. E 85 21909
22 Xia Z, Bell D R, Shi Y and Ren P Y 2013 J. Phys. Chem. B 117 3135
23 Kim N, Laing C, Elmetwaly S, Jung S, Curuksu J, Schlick T 2014 Proc. Natl. Acad. Sci. USA 111 4079
24 Xu X, Zhao P and Chen S 2014 PloS one 9 e107504
25 Shi Y Z, Wang F H, Wu Y Y and Tan Z J 2014 J. Chem. Phys. 141 105102
26 Shi Y Z, Wang F H, Wu Y Y and Tan Z J2014 J. Chem. Phys. 141 105102
27 Shi Y Z, Jin L, Wang F H, Zhu X L and Tan Z J 2015 Biophys. J. 109 2654
28 Boniecki M J, Lach G, Dawson W K, Tomala K, Lukasz P, Soltysinski T, Rother K M and Bujnicki J M 2016 Nucleic Acids Res. 44 e63
29 Li J, Zhang J, Wang J, Li W and Wang W 2016 PLoS Comput. Biol. 12 e1005032
30 Jain S and Schlick T 2017 J. Mol. Biol. 429 3587
31 Bell D R, Cheng S Y, Salazar H and Ren P 2017 Sci. Rep. 7 45812
32 Wang J, Mao K, Zhao Y, Zeng C, Xiang J, Zhang Y and Xiao Y 2017 Nucleic Acids Res. 45 6299
33 Jin L, Shi Y Z, Feng C J, Tan Y L and Tan Z J 2018 Biophys. J. 115 1403
34 Shi Y Z, Jin L, Feng C J, Tan Y L and Tan Z J 2018 PLoS Comp. Biol. 14 e1006222
35 Zhang B, Qiu H, Jiang J, Liu J and Shi Y Z 2019 J. Chem. Phys. 151 165101
36 Jin L, Tan Y L, Wu Y, Wang X, Shi Y Z and Tan Z J 2019 RNA 25 1532
37 Zhang J, Dundas J, Lin M, Chen R, Wang W and Liang J 2009 RNA 12 2248
38 Jonikas M A, Radmer R J, Laederach A, Das R, Pearlman S, Herschlag D and Altman R B 2009 RNA 15 189
39 Zhang D and Chen S J 2018 J. Chem. Theory Comput. 14 2230
40 Tanaka S and Scheraga H A 1976 Macromolecules 9 945
41 Sippl M J 1990 J. Mol. Biol. 213 859
42 Thomas P D and Dill K A 1996 J. Mol. Biol. 257 457
43 Melo F and Feytmans E 1997 J. Mol. Biol. 267 207
44 Samudrala R, Moult J 1998 J. Mol. Biol. 275 895
45 Skolnick J, Kolinski A and Ortiz A 2000 Proteins 38 3
46 Buchete N V, Straub J E and Thirumalai D 2004 Curr. Opin. Struct. Biol. 14 225
47 Chi Z, Song L, Zhu Q and Zhou Y Q 2005 J. Med. Chem. 48 2325
48 Huang S Y and Zou X Q 2011 Proteins 79 2648
49 Deng H, Jia Y, Wei Y and Zhang Y 2012 Proteins: Struct. Funct. Genet. 80 2311
50 Dima R I, Hyeon C and Thirumalai D 2005 J. Mol. Biol. 347 53
51 Bernauer J, Huang X, Sim A Y L and Levitt M 2011 RNA 17 1066
52 Capriotti E, Norambuena T, Marti-Renom M A and Melo F 2011 Bioinformatics 27 1086
53 Wang J, Zhao Y, Zhu C and Xiao Y 2015 Nucleic Acids Res. 43 e63
54 Li J, Zhu W, Wang J, L W, Gong S, Zhang J and Wang W 2018 PLoS Comput. Biol. 14 e1006514
55 Yang Y, Gu Q, Zhang B, Shi Y Z, Shao Z G 2018 Chin. Phys. B 27 38701
56 Tan Y L, Feng C J, Jin L, Shi Y Z and Tan Z J 2019 RNA 25 793
57 Masso M J 2018 Theor Biol. 453 58
58 Miyazawa S and Jernigan R L 1985 Macromolecules 18 534
59 Sippl M J 1993 J. Comput. Aid Mol. Des. 7 473
60 Anfinsen C B.1973 Science 181 223
61 Sippl M J 1995 Curr. Opin. Struct. Biol. 5 229
62 Nishikawa K and Matsuo Y O 1993 Protein Eng. 6 811
63 Kocher J P A, Rooman M J and Wodak S J 1994 J. Mol. Biol. 235 1598
64 Singh R K, Tropsha A and Vaisman I I 1996 J. Comp. Biol. 3 213
65 Miyazawa S and Jernigan R L 2005 J. Chem. Phys. 122 24901
66 Lu H and Skolnick J 2001 Proteins: Struct. Funct. Bioinform. 44 223
67 Zhou H and Zhou Y 2002 Protein Sci. 11 2714
68 Shen M Y and Sali A 2006 Protein Sci. 15 2507
69 Rykunov D and Fiser A 2010 BMC Bioinformatics 11 128
70 Zhang J and Zhang Y 2010 PloS One 5 e15386
71 Huang S Y and Zou X Q 2008 Proteins: Struct. Funct. Bioinform. 72 557
72 Huang S Y and Zou X Q 2006 J. Comput. Chem. 27 1866
73 Gromiha M M and Selvaraj S 2004 Prog. Biophys. Mol. Biol. 86 235
74 Gromiha M M and Selvaraj S. 1999 Biophys. Chem. 77 49
75 Gromiha M M and Selvaraj S. 1997 J. Biol. Phys. 23 151
76 Carter C W, Lefebvre B C, Cammer S A, Tropsha A, Edgell M H 2001 J. Mol. Biol. 311 625
77 Li X, Hu C, Liang J 2003 Proteins: Struct. Funct. Bioinform. 53 792
78 Krishnamoorthy B and Tropsha A 2003 Bioinformatics 19 1540
79 Feng Y, Kloczkowski A and Jernigan R L 2007 Proteins: Struct. Funct. Bioinform. 68 57
80 Gniewek P, Leelananda S P, Kolinski A, Jernigan R L and Kloczkowski A 2011 Proteins: Struct. Funct. Bioinform. 79 1923
81 Lu M, Dousis A D and Ma J 2008 J. Mol. Biol. 376 288
82 Yu Z, Yao Y, Deng H and Yi M 2019 BMC Bioinformatics 20 211
83 Zhou H and Skolnick J 2011 Biophys. J. 101 2043
84 Lòpez-Blanco J R and Chacòn P 2019 Bioinformatics 35 3013
85 Kortemme T, Morozov A V and Baker D 2003 J. Mol. Biol. 326 1239
86 Yang Y and Zhou Y 2008 Proteins: Struct. Funct. Bioinform. 72 793
87 Wang X and Huang S Y 2019 J. Chem. Inf. Model. 59 3080
88 Buchete N V, Straub J E and Thirumalai D 2004 Protein Sci. 13 862
89 Friedman H L 1985 A Course in Statistical Mechanics (Prentice-Hall, Englewood Cliffs)
90 Kumarevel T S, Gromiha M M, Selvaraj S, Gayatri K, Kumar P K R 2002 Biophys. Chem. 99 189
91 Miyazawa S and Jernigan R L 1999 Proteins 36 347
92 Rooman M J, Kocher J P A and Wodak S J 1992 Biochemistry 31 10226
93 Kocher J P, Rooman M J and Wodak S J 1994 J. Mol. Biol. 235 1598
94 Gilis D and Rooman M 1997 J. Mol. Biol. 272 276
95 Melo F, Sanchez R and Sali A 2002 Protein Sci. 11 430
96 Munson P J and Singh R K 1997 Protein Sci. 6 1467
97 Li X and Liang J 2005 Proteins: Struct. Funct. Bioinform. 60 46
98 Masso M 2017 Biomed. Res. Int. 5760612
99 Barber C B, Dobkin D P and Huhdanpaa H 1996 Acm. T. Math. Software 22 469
100 Eastwood M P and Wolynes P G 2001 J. Chem. Phys. 114 4702
101 Rossi A, Micheletti C, Seno F and Maritan A 2001 Biophys. J. 80 480
102 Godzik A and Skolnick J 1992 Proc. Natl. Acad. Sci. USA 89 12098
103 Liu Y, Zeng J and Gong H 2014 Proteins 82 2383
104 Wu Y Y, Bao L, Zhang X and Tan Z J 2015 J. Chem. Phys. 142 125103
105 Zhang X, Bao L, Wu Y Y, Zhu X L and Tan Z J 2017 J. Chem. Phys. 147 054901
106 Hyeon C, Dima R I and Thirumalai D 2006 J. Chem. Phys. 125 194905
107 Xiong G, Xi K, Zhang X and Tan Z J 2018 Chin. Phys. B 27 018203
108 Chen S J 2008 Annu. Rev. Biophys. 37 197
109 Tan Z J and Chen S J 2010 Biophys. J. 2010 99 1565
110 Tan Z J and Chen S J 2011 Biophys. J. 101 176
111 Lipfert J, Doniach S, Das R and Herschlag D 2014 Annu. Rev. Biochem. 83 813
112 Wu Y Y, Zhang Z L, Zhang J S, Zhu X L and Tan Z J 2015 Nucleic Acids Res. 43 6156
113 Xi K, Wang F H, Xiong G, Zhang Z L and Tan Z J 2018 Biophys. J. 114 1776
114 Bao L, Zhang X, Jin L and Tan Z J 2016 Chin. Phys. B 25 18703 |
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