[1] |
Chaplin M 2006 Nat. Rev. Mol. Cell Bio. 7 861
doi: 10.1038/nrm2021
|
[2] |
Huang Z Q, Yang R Y, Jiang W Z and Zhang Q L 2016 Chin. Phys. Lett. 33 013101
doi: 10.1088/0256-307X/33/1/013101
|
[3] |
Abolfath R M, van Duin A C T and Brabec T 2011 J. Phys. Chem. A 115 11045
doi: 10.1021/jp204894m
|
[4] |
Wang X, Li M, Ye F F and Zhou X 2017 Acta Phys. Sin. 66 150201(inChinese)
|
[5] |
Cyphers S, Ruff E F, Behr J M, Chodera J D and Levinson N M 2017 Nat. Chem. Biol. 13 402
doi: 10.1038/nchembio.2296
|
[6] |
Ulrich K, Galvosas P, Kärger J and Grinberg F 2009 Phys. Rev. Lett. 102 037801
doi: 10.1103/PhysRevLett.102.037801
|
[7] |
Fernández A 2014 J. Chem. Phys. 140 221102
doi: 10.1063/1.4882895
|
[8] |
Lynden-Bell R M and Debenedetti P G 2005 J. Phys. Chem. B 109 6527
|
[9] |
Ball P 2005 Nature 436 1084
doi: 10.1038/4361084a
|
[10] |
Gu B, Zhang F S, Wang Z P and Zhou H Y 2008 Phys. Rev. Lett. 100 088104
doi: 10.1103/PhysRevLett.100.088104
|
[11] |
Errington J R and Debenedetti P G 2001 Nature 409 318
doi: 10.1038/35053024
|
[12] |
Chakraborty D and Wales D J 2017 Phys. Chem. Chem. Phys. 19 878
doi: 10.1039/C6CP06309H
|
[13] |
Samanta S, Mukherjee S, Chakrabarti J and Bhattacharyya D 2009 J. Chem. Phys. 130 115103
doi: 10.1063/1.3078797
|
[14] |
Banavali N K and Roux B 2005 J. Am. Chem. Soc. 127 6866
doi: 10.1021/ja050482k
|
[15] |
Lange A W and Herbert J M 2009 J. Am. Chem. Soc. 131 3913
doi: 10.1021/ja808998q
|
[16] |
Shen X, Atamas N A and Zhang F S 2012 Phys. Rev. E 85 051913
doi: 10.1103/PhysRevE.85.051913
|
[17] |
Maaloum M, Beker A F and Muller P 2011 Phys. Rev. E 83 031903
doi: 10.1103/PhysRevE.83.031903
|
[18] |
Wang Y W and Yang G C 2017 Chin. Phys. B 26 128706
doi: 10.1088/1674-1056/26/12/128706
|
[19] |
Lindahl T 2016 Nat. Rev. Mol. Cell Bio. 17 335
|
[20] |
Eliasson R, Hammarsten E and Lindahl T 1962 Biotechnol. Bioeng. 4 53
doi: 10.1002/bit.260040107
|
[21] |
Anagnostopoulos C and Spizizen J 1961 J. Bacteriol. 81 741
|
[22] |
Pogozelski W K and Tullius T D 1998 Chem. Rev. 98 1089
doi: 10.1021/cr960437i
|
[23] |
Tullius T D and Greenbaum J A 2005 Curr. Opin. Chem. Biol. 9 127
doi: 10.1016/j.cbpa.2005.02.009
|
[24] |
Aydogan B, Bolch W E, Swarts S G, Turner J E and David T 2008 Radiat. Res. 169 223
doi: 10.1667/RR0293.1
|
[25] |
Friedland W, Jacob P, Paretzke H G, Merzagora M and Ottolenghi A1999 Radiat. Environ. Biophys. 38 39
|
[26] |
Abolfath R M, Biswas P K, Rajnarayanam R, Brabec T, Kodym R andPapiez L 2012 J. Phys. Chem. A 116 3940
doi: 10.1021/jp300258n
|
[27] |
Merzel F, Fontaine-Vive F, Johnson M R and Kearley G J 2007 Phys. Rev. E 76 031917
doi: 10.1103/PhysRevE.76.031917
|
[28] |
Smirnov D A, Morley M, Shin E, Spielman R S and Cheung V G 2009 Nature 459 587
doi: 10.1038/nature07940
|
[29] |
Rak J, Chomicz L, Wiczk J, Westphal K, Zdrowowicz M, Wityk P,Zyndul M, Makurat S and Golon Ł 2015 J. Phys. Chem. B 119 8227
doi: 10.1021/acs.jpcb.5b03948
|
[30] |
Hamelberg D, McFail-Isom L, Williams L D and Wilson W D 2000 J. Am. Chem. Soc. 122 10513
doi: 10.1021/ja000707l
|
[31] |
Korolev N, Lyubartsev A P, Laaksonen A and Nordenskiold L 2003 Nucleic Acids Res. 31 5971
doi: 10.1093/nar/gkg802
|
[32] |
Noy A, Pérez A, Laughton C A and Orozco M 2007 Nucleic Acids Res. 35 3330
doi: 10.1093/nar/gkl1135
|
[33] |
Pastor N 2005 Biophys. J. 88 3262
doi: 10.1529/biophysj.104.058339
|
[34] |
Freddolino P L, Arkhipov A S, Larson S B, McPherson A and Schultem K 2006 Structure 14 437
doi: 10.1016/j.str.2005.11.014
|
[35] |
Shen H, Cheng W and Zhang F S 2015 RSC Adv. 5 9627
doi: 10.1039/C4RA14739A
|
[36] |
Martínez L, Andrade R, Birgin E G and Martínez J M 2009 J. Comput. Chem. 30 2157
doi: 10.1002/jcc.21224
|
[37] |
Schweitzer B I, Mikita T, Kellogg G W, Gardner K H and Beardsley GP 1994 Biochemistry 33 11460
doi: 10.1021/bi00204a008
|
[38] |
Dans P D, Danilāne L, Ivani I, Dršata T, Lankaš F, Hospital A, Walther J, Pujagut R I, Battistini F, Gelpí J L, Lavery R and Orozco M 2016 Nucleic Acids Res. 44 4052
doi: 10.1093/nar/gkw264
|
[39] |
Pérez A, Luque F J and Orozco M 2007 J. Am. Chem. Soc. 129 14739
doi: 10.1021/ja0753546
|
[40] |
Dršata T, Pérez A, Orozco M, Morozov A V, Šponer J and Lankaš F 2013 J. Chem Theory Comput. 9 707
doi: 10.1021/ct300671y
|
[41] |
Mark P and Nilsson L 2002 J. Phys. Chem. B 106 9440
doi: 10.1021/jp025965e
|
[42] |
Ivani I, Dans P D, Noy A, Pérez A, Faustino I, Hospital A, Walther J, Andrio P, Goñi R, Balaceanu A, Portella G, Battistini F, Gelpí J L,González C, Vendruscolo M, Laughton C A, Harris S A, Case D A and Orozco M 2016 Nat. Methods 13 55
doi: 10.1038/nmeth.3658
|
[43] |
Darden T, York D and Pedersen L 1998 J. Chem. Phys. 98 10089
|
[44] |
Allen M P and Tildesley D J 1989 Computer Simulation of Liquids (Oxford University Press)
|
[45] |
Hess B, Bekker H, Berendsen H J C and Fraaije J G E M 1997 J. Comput. Chem. 18 1463
doi: 10.1002/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H
|
[46] |
Berendsen H J C, Grigera J R and Straatsma T P 1987 J. Phys. Chem. 91 6269
doi: 10.1021/j100308a038
|
[47] |
Zhang F S and Lynden-Bell R M 2005 Phy. Rev. E 71 021502
doi: 10.1103/PhysRevE.71.021502
|
[48] |
Lindahl E, Hess B and van der Spoel D 2001 J. Mol. Model. 7 306
doi: 10.1007/s008940100045
|
[49] |
Tsierkezos N G and Molinou I E 1998 J. Chem. Eng. Data 43 989
doi: 10.1021/je9800914
|
[50] |
Nose S and Klein M L 1983 Mol. Phys. 50 1055
doi: 10.1080/00268978300102851
|
[51] |
Berendsen H J C, Postma J P M, van Gunsteren W F, DiNola A andHaak J R 1984 J. Chem. Phys. 81 3684
doi: 10.1063/1.448118
|
[52] |
Lavery R, Moakher M, Maddocks J H, Petkeviciute D and ZakrzewskaK 2009 Nucleic Acids Res. 37 5917
doi: 10.1093/nar/gkp608
|
[53] |
Lavery R and Sklenar H 1989 J. Biomol. Struct. Dyn. 6 655
doi: 10.1080/07391102.1989.10507728
|
[54] |
Kumar R, Schmidt J R and Skinner J L 2007 J. Chem. Phys. 126 204107
doi: 10.1063/1.2742385
|
[55] |
Herskovits T T 1962 Arch. Biochem. Biophys. 97 474
doi: 10.1016/0003-9861(62)90110-8
|
[56] |
Zgarbová M, Otyepka M, Šponer J, Lankaš F and Jurečka P 2014 J. Chem. Theory Comput. 10 3177
doi: 10.1021/ct500120v
|
[57] |
Leroy J L, Kochoyan M, Huynh-Dinh T and Guéron M 1988 J. Mol. Biol. 200 223
doi: 10.1016/0022-2836(88)90236-7
|
[58] |
Andreatta D, Sen S, Lustres J L P, Kovalenko S A, Ernsting N P, Murphy C J, Coleman R S and Berg M A 2006 J. Am. Chem. Soc. 128 6885
doi: 10.1021/ja0582105
|
[59] |
McConnell K J and Beveridge D L 2000 J. Mol. Biol. 304 803
doi: 10.1006/jmbi.2000.4167
|
[60] |
Dickerson R E, Drew H R, Conner B N, Wing R M, Fratini A V andKopka M L 1982 Science 216 475
doi: 10.1126/science.7071593
|
[61] |
Allahyarov E, Gompper G and Lowen H 2013 Phys. Rev. E 69 041904
|
[62] |
Saenger W, Hunter W N and Kennard O 1986 Nature 324 385
doi: 10.1038/324385a0
|
[63] |
Hartmann B, Piazzola D and Lavery R 1993 Nucleic Acids Res. 21 561
doi: 10.1093/nar/21.3.561
|
[64] |
Schwieters C D and Clore G M 2007 Biochemistry 46 1152
doi: 10.1021/bi061943x
|
[65] |
Djuranovic D and Hartmann B 2004 Biopolymers 73 356
doi: 10.1002/bip.10528
|
[66] |
Heddi B, Oguey C, Lavelle C, Foloppe N and Hartmann B 2010 Nucleic Acids Res. 38 1034
doi: 10.1093/nar/gkp962
|
[67] |
Wecker K, Bonnet M C and Meurs E F 2002 Nucleic Acids Res. 30 4452
doi: 10.1093/nar/gkf559
|
[68] |
Madhumalar A and Bansal M 2005 J. Biomol. Struct. Dyn. 23 13
doi: 10.1080/07391102.2005.10507043
|
[69] |
Dans P D, Faustino I, Battistini F, Zakrzewska K, Lavery R and OrozcoM 2014 Nucleic Acids Res. 42 11304
doi: 10.1093/nar/gku809
|