[1] Wang E, Sun H, Wang J, Wang Z, Liu H, Zhang J Z H and Hou T 2019 Chem. Rev. 119 9478 [2] Genheden S and Ryde U 2015 Expert. Opin. Drug. Dis. 10 449 [3] Wang C, Greene D, Xiao L, Qi R and Luo R 2018 Front. Mol. Biosci. 4 87 [4] Homeyer N and Gohlke H 2012 Mol. Inform. 31 114 [5] Williamsnoonan B J, Yuriev E and Chalmers D K 2017 J. Med. Chem. 61 638 [6] Chodera J D, Mobley D L, Shirts M R, Dixon R W, Branson K and Pande V S 2011 Curr. Opin. Struc. Biol. 21 150 [7] Pohorille A, Jarzynski C and Chipot C 2010 J. Phys. Chem. B 114 10235 [8] Pu C, Yan G, Shi J and Li R 2017 Med. Chem. Comm. 8 1452 [9] Sun H, Li Y, Shen M, Tian S, Xu L, Pan P, Guan Y and Hou T 2014 Phys. Chem. Chem. Phys. 16 22035 [10] Hou T, Wang J, Li Y and Wang W 2011 J. Comput. Chem. 32 866 [11] Ahinko M, Niinivehmas S, Jokinen E M and Pentikainen O T 2019 Chem. Biol. Drug. Des. 93 522 [12] Hou T, Wang J, Li Y and Wang W 2011 J. Chem. Inf. Model. 51 69 [13] Liu J, He X and Zhang J Z H 2013 J. Chem. Inf. Model. 53 1306 [14] Wang E, Liu H, Wang J, Weng G, Sun H, Wang Z, Kang Y and Hou T 2020 J. Chem. Inf. Model. 60 5353 [15] Mikulskis P, Genheden S and Ryde U 2014 J. Chem. Inf. Model. 54 2794 [16] Greenidge P, Kramer C, Mozziconacci J and Wolf R M 2013 J. Chem. Inf. Model. 53 201 [17] Wang E, Weng G, Sun H, Du H, Zhu F, Chen F, Wang Z and Hou T 2019 Phys. Chem. Chem. Phys. 21 18958 [18] Maffucci I and Contini A 2016 J. Chem. Inf. Model. 56 1692 [19] Liu X, Peng L and Zhang J Z H 2019 J. Chem. Inf. Model. 59 272 [20] Sun Z, Yan Y N, Yang M and Zhang J Z H 2017 J. Chem. Phys. 146 124124 [21] Chen F, Sun H, Wang J, Zhu F, Liu H, Wang Z, Lei T, Li Y and Hou T 2018 RNA 24 1183 [22] Sun H, Li Y, Tian S, Xu L and Hou T 2014 Phys. Chem. Chem. Phys. 16 16719 [23] Ravindranathan K P, Tiradorives J, Jorgensen W L and Guimaraes C R W 2011 J. Chem. Theory Comput. 7 3859 [24] Li Y, Cong Y, Feng G, Zhong S, Zhang J Z H, Sun H and Duan L 2018 Struct. Dynam. 5 064101 [25] Sheng Y J, Yin Y W, Ma Y Q and Ding H M 2021 J. Chem. Inf. Model. 61 2454 [26] Ding H M, Yin Y W, Ni S D, Sheng Y J and Ma Y Q 2021 Chin. Phys. Lett. 38 018701 [27] Manning G S 1969 J. Chem. Phys. 51 924 [28] Liljas A, Liljas L, Piskur J, Linblom G, Nissen P and Kjeldgaard M 2009 Textbook of Structural Biology (Singapore:World Scientific Publishing) [29] Ding H, Li J, Chen N, Hu X, Yang X, Guo L, Li Q, Zuo X, Wang L and Ma Y 2018 ACS Central. Sci. 4 1344 [30] Douglas S M, Dietz H, Liedl T, Hogberg B, Graf F and Shih W M 2009 Nature 459 414 [31] Hu Q, Li H, Wang L, Gu H and Fan C 2018 Chem. Rev. 119 6459 [32] Orphanides G and Reinberg D 2002 Cell 108 439 [33] Liu Z, Su M, Han L, Liu J, Yang Q, Li Y and Wang R 2017 Acc. Chem. Res. 50 302 [34] Wang R, Fang X, Lu Y and Wang S 2004 J. Med. Chem. 47 2977 [35] Jorgensen W L and Madura J D 1983 J. Am. Chem. Soc. 105 1407 [36] Der Spoel D V, Lindahl E, Hess B, Groenhof G, Mark A E and Berendsen H J C 2005 J. Comput. Chem. 26 1701 [37] Abraham M J, Murtola T, Schulz R, Pall S, Smith J C, Hess B and Lindahl E 2015 SoftwareX 1-2 19 [38] Maier J, Martinez C, Kasavajhala K, Wickstrom L, Hauser K and Simmerling C 2015 J. Chem. Theory Comput. 11 3696 [39] Hess B, Bekker H, Berendsen H J C and Fraaije J G E M 1997 J. Comput. Chem. 18 1463 [40] Essmann U, Perera L, Berkowitz M L, Darden T, Lee H and Pedersen L G 1995 J. Chem. Phys. 103 8577 [41] Bussi G, Donadio D and Parrinello M 2007 J. Chem. Phys. 126 014101 [42] Parrinello M and Rahman A 1981 J. Appl. Phys. 52 7182 [43] https://jerkwin.github.io/gmxtool |