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 |