Chinese Physics B, Volume. 29, Issue 10, (2020)

Methods and applications of RNA contact prediction

Huiwen Wang and Yunjie Zhao
Author Affiliations
  • Institute of Biophysics and Department of Physics, Central China Normal University, Wuhan 430079, China
  • show less
    References(92)

    [1] J Wang, Y Zhao, C Zhu, Y Xiao. Nucleic Acids Res., 43, e63(2015).

    [2] J Wang, K Mao, Y Zhao, C Zeng, J Xiang, Y Zhang, Y Xiao. Nucleic Acids Res., 45, 6299(2017).

    [3] L Zelinger, A Swaroop. Trends Genet., 34, 341(2018).

    [4] D Lu, T Thum. Nat. Rev. Cardiol., 16, 661(2019).

    [5] Y Huang, H Li, Y Xiao. Bioinformatics, 34, 1238(2018).

    [6] J Zhang, Y J Zhang, W Wang. Chin. Phys. Lett., 27(2010).

    [7] C Nithin, P Ghosh, J M Bujnicki. Genes, 9, 432(2018).

    [8] H Wang, K Wang, Z Guan, Y Jian, Y Jia, F Kashanchi, C Zeng, . Chin. Phys. B, 26(2017).

    [9] Y Yan, S Y Huang. Bioinformatics, 34, 453(2018).

    [10] Y Yan, D Zhang, P Zhou, B Li, S Y Huang. Nucleic Acids Res., 45, W365(2017).

    [11] Y Zhao, Y Jian, Z Liu, H Liu, Q Liu, C Chen, Z Li, L Wang, H H Huang, C Zeng. Sci. Rep., 7, 2876(2017).

    [12] Y Yan, Z Wen, D Zhang, S Y Huang. Nucleic Acids Res., 46, e56(2018).

    [13] L Bao, J Wang, Y Xiao. Phys. Rev. E, 100(2019).

    [14] H Wang, J Qiu, H Liu, Y Jian, Y Xu, Y Jia, F Kashanchi, C Zeng, Y Zhao. BMC Bioinformatics, 20, 617(2019).

    [15] J Karn, N J Keen, M J Churcher, F Aboul-ela, G Varani, F Hamy, E R Felder, G Heizmann, T Klimkait. Pharmacochemistry Library, 29, 121(1998).

    [16] F A Abulwerdi, S F J L Grice. Curr. Pharm. Des., 23, 4112(2017).

    [17] Y Zhao, H Chen, C Du, Y Jian, H Li, Y Xiao, M Saifuddin, F Kashanchi, C Zeng. Int. J. Pept. Res. Ther., 25, 807(2018).

    [18] P Romby, E Charpentier. Cell. Mol. Life Sci., 67, 217(2010).

    [19] T Zhou, H Wang, L Song, Y Zhao. J. Theor. Comput. Chem., 19(2020).

    [20] Y Lou, B Chen, J Zhou, H O Sintim, T K Dayie. Mol.Biosyst., 10, 384(2014).

    [21] M Kang, C D Eichhorn, J Feigon. Proc. Natl. Acad. Sci. USA, 111, E663(2014).

    [22] A K Heroven, A M Nuss, P Dersch. RNA Biol., 14, 471(2017).

    [23] H Wang, Z Guan, J Qiu, Y Jia, C Zeng, Y Zhao. RSC. Adv., 10, 2004(2020).

    [24] L Jiang, C Schaffitzel, R Bingel-Erlenmeyer, N Ban, P Korber, R I Koning, C de Geus Dd, J R Plaisier, J P Abrahams. J. Mol. Biol., 386, 1357(2009).

    [25] J H Cate, J A Doudna. Method. Enzymol., 317, 169(2000).

    [26] M P Latham, D J Brown, S A McCallum, A Prodi. Chembiochem, 6, 1492(2005).

    [27] Y Zhao, J Wang, C Zeng, Y Xiao. Biophys. Rep., 4, 123(2018).

    [28] Y Tang, D Liu, Z Wang, T Wen, L Deng. BMC Bioinformatics, 18, 465(2017).

    [29] H Su, M Liu, S Sun, Z Peng, J Yang. Bioinformatics, 35, 930(2019).

    [30] O Duss, M Yulikov, G Jeschke, F H Allain. Nat. Commun., 5, 3669(2014).

    [31] O Duss, M Yulikov, F H T Allain, G Jeschke. Method. Enzymol., 558, 279(2015).

    [32] H K Cheong, E Hwang, C Lee, B S Choi, C Cheong. Nucleic Acids Res., 32, e84(2004).

    [33] Y Zhao, Y Huang, G Zhou, Y Wang, J Man, Y Xiao. Sci. Rep., 2, 734(2012).

    [34] J Wang, Y Xiao. Current Protocols in Bioinformatics, 57, 5.9.1(2017).

    [35] J Wang, J Wang, Y Huang, Y Xiao. Int. J. Mol. Sci., 20, 4116(2019).

    [36] Z Gong, Y Zhao, Y Xiao. J. Biomol. Struc. Dyn., 28, 431(2010).

    [37] Y Zhao, G Zhou, Y Xiao. J. Biomol. Struc. Dyn., 28, 815(2011).

    [38] S Sharma, F Ding, N V Dokholyan. Bioinformatics, 24, 1951(2008).

    [39] A Krokhotin, K Houlihan, N V Dokholyan. Bioinformatics, 31, 2891(2015).

    [40] J He, J Wang, H Tao, Y Xiao, S Y Huang. Nucleic Acids Res., 47, W35(2019).

    [41] L Bao, X Zhang, L Jin, Z J Tan. Chin. Phys. B, 25(2015).

    [42] N A Siegfried, S Busan, G M Rice, J A Nelson, K M Weeks. Nat. Methods, 11, 959(2014).

    [43] M E Harris, E L Christian. Methods Enzymol., 468, 127(2009).

    [44] M Hafner, M Landthaler, L Burger, M Khorshid, J Hausser, P Berninger, A Rothballer, M Ascano, A C Jungkamp, M Munschauer, A Ulrich, G S Wardle, S Dewell, M Zavolan, T Tuschl. Cell, 141, 129(2010).

    [45] J Zhao, T K Ohsumi, J T Kung, Y Ogawa, D J Grau, K Sarma, J J Song, R E Kingston, M Borowsky, J T Lee. Mol. Cell, 40, 939(2010).

    [46] T W Nilsen. Cold Spring Harb. Protoc., 2014, 683(2014).

    [47] C Stork, S Zheng. Reporter Gene Assays Reporter Gene Assays, 65-74(2018).

    [48] Y Z Shi, Y Y Wu, F H Wang, Z J Tan. Chin. Phys. B, 23(2014).

    [49] Y Yang, Q Gu, B G Zhang, Y Z Shi, Z G Shao. Chin. Phys. B, 27(2018).

    [50] F Mueller, T Döring, T Erdemir, B Greuer, N Jünke, M Osswald, J Rinke-Appel, K Stade, S Thamm, R Brimacombe. Biochem. Cell Biol., 73, 767(1995).

    [51] C Massire, E Westhof. J. Mol. Graph. Model., 16, 197(1998).

    [52] F Jossinet, E Westhof. Bioinformatics, 21, 3320(2005).

    [53] H M Martinez, J V Maizel, B A Shapiro. J. Biomol. Struct. Dyn., 25, 669(2008).

    [54] F Jossinet, T E Ludwig, E Westhof. Bioinformatics, 26, 2057(2010).

    [55] S Cao, S J Chen. RNA, 11, 1884(2005).

    [56] M Parisien, F Major. Nature, 452, 51(2008).

    [57] S C Flores, R B Altman. RNA, 16, 1769(2010).

    [58] M Rother, K Rother, T Puton, J M Bujnicki. Nucleic Acids Res., 39, 4007(2011).

    [59] M Biesiada, K J Purzycka, M Szachniuk, J Blazewicz, R W Adamiak. RNA Structure Determination, 199-215(2016).

    [60] R Das, D Baker. Proc. Natl. Acad. Sci. USA, 104(2007).

    [61] M A Jonikas, R J Radmer, A Laederach, R Das, S Pearlman, D Herschlag, R B Altman. RNA, 15, 189(2009).

    [62] R Das, J Karanicolas, D Baker. Nat. Methods, 7, 291(2010).

    [63] M J Boniecki, G Lach, W K Dawson, K Tomala, P Lukasz, T Soltysinski, K M Rother, J M Bujnicki. Nucleic Acids Res., 44, e63(2016).

    [64] R R Gutell, A Power, G Z Hertz, E J Putz, G D Stormo. Nucleic Acids Res., 20, 5785(1992).

    [65] E Freyhult, V Moulton, P Gardner. Appl. Bioinformatics, 4, 53(2005).

    [66] S D Dunn, L M Wahl, G B Gloor. Bioinformatics, 24, 333(2008).

    [67] R C Edgar. Nucleic Acids Res., 32, 1792(2004).

    [68] R Chenna, H Sugawara, T Koike, R Lopez, T J Gibson, D G Higgins, J D Thompson. Nucleic Acids Res., 31, 3497(2003).

    [69] D G Higgins, P M Sharp. Gene, 73, 237(1988).

    [70] K Katoh, K Kuma, H Toh, T Miyata. Nucleic Acids Res., 33, 511(2005).

    [71] R C Edgar, S Batzoglou. Curr. Opin. Struc. Biol., 16, 368(2006).

    [72] C Notredame, D G Higgins, J Heringa. J. Mol. Biol., 302, 205(2000).

    [73] T Lassmann. Bioinformatics, 36, 1928(2020).

    [74] F Morcos, A Pagnani, B Lunt, A Bertolino, D S Marks, C Sander, R Zecchina, J N Onuchic, T Hwa, M Weigt. Proc. Natl. Acad. Sci. USA, 108(2011).

    [75] E De Leonardis, B Lutz, S Ratz, S Cocco, R Monasson, A Schug, M Weigt. Nucleic Acids Res., 43(2015).

    [76] C Weinreb, A J Riesselman, J B Ingraham, T Gross, C Sander, D S Marks. Cell, 165, 963(2016).

    [77] M Weigt, R A White, H Szurmant, J A Hoch, T Hwa. PNAS., 106, 67(2009).

    [78] C Weinreb, A J Riesselman, J B Ingraham, T Gross, C Sander, D S Marks. Cell, 165, 963(2016).

    [79] Y Jian, X Wang, J Qiu, H Wang, Z Liu, Y Zhao, C Zeng. BMC Bioinformatics, 20, 497(2019).

    [80] G E Hinton. Neural Networks: Tricks of the Trade, 599-619(2012).

    [81] S J De Vries, M Van Dijk, A M J J Bonvin. Nat. Protoc., 5, 883(2010).

    [82] O Trott, A J Olson. J. Comput. Chem., 31, 445(2010).

    [83] C Dominguez, R Boelens, A M Bonvin. J. Am. Chem. Soc., 125, 1731(2003).

    [84] J He, H Tao, S Y Huang. Bioinformatics, 35, 4994(2019).

    [85] P Zeng, J Li, W Ma, Q Cui. Sci. Rep., 5, 9179(2015).

    [86] P Zeng, Q Cui. Sci. Rep., 6(2016).

    [87] K Wang, Y Jian, H Wang, C Zeng, Y Zhao. Bioinformatics, 34, 3131(2018).

    [88] N Tuvshinjargal, W Lee, B Park, K Han. Comput. Meth. Prog. Bio., 120, 3(2015).

    [89] N Tuvshinjargal, W Lee, B Park, K Han. Biosystems, 139, 17(2016).

    [90] X He, Wang Jun, J Wang, Y Xiao. Chin. Phys. B, 29(2020).

    [91] S Griffithsjones, A Bateman, M Marshall, A Khanna, S R Eddy. Nucleic Acids Res., 31, 439(2003).

    [92] U Schulze-Gahmen, I Echeverria, G Stjepanovic, Y Bai, H Lu, D Schneidman-Duhovny, J A Doudna, Q Zhou, A Sali, J H Hurley. Elife, 5(2016).

    Tools

    Get Citation

    Copy Citation Text

    Huiwen Wang, Yunjie Zhao. Methods and applications of RNA contact prediction[J]. Chinese Physics B, 2020, 29(10):

    Download Citation

    EndNote(RIS)BibTexPlain Text
    Save article for my favorites
    Paper Information

    Received: Apr. 30, 2020

    Accepted: --

    Published Online: Apr. 21, 2021

    The Author Email: Zhao Yunjie (yjzhaowh@mail.ccnu.edu.cn)

    DOI:10.1088/1674-1056/abb7f3

    Topics