[1] |
Bryngelson J D and Wolynes P G 1987 Proc. Natl. Acad. Sci. USA 847524
|
[2] |
Bryngelson J D and Wolynes P G 1989 J. Phys. Chem. 93 6902
|
[3] |
Bryngelson J D and Wolynes P G 1990 Biopolymers 30 177
|
[4] |
Onuchic J N, Wolynes P G, Lutheyschulten Z and Socci N D 1995Proc. Natl. Acad. Sci. USA 92 3626
|
[5] |
Onuchic J N, LutheySchulten Z and Wolynes P G 1997 Annu. Rev.Phys. Chem. 48 545
|
[6] |
Dill K A and Chan H S 1997 Nat. Struct. Biol. 4 10
|
[7] |
Dobson C M, Sali A and Karplus M Š 1998 Angew. Chem. Int. Ed. 37868
|
[8] |
Wang J 2015 Adv. Phys. 64 1
|
[9] |
Wang J, Xu L and Wang E K 2008 Proc. Natl. Acad. Sci. USA 10512271
|
[10] |
Wang J, Li C H and Wang E K 2010 Proc. Natl. Acad. Sci. USA 1078195
|
[11] |
Li C H and Wang J 2014 Proc. Natl. Acad. Sci. USA 111 14130
|
[12] |
Wang J, Xu L, Wang E K and Huang S 2010 Biophys. J. 99 29
|
[13] |
Wang J, Zhang K and Wang E K 2010 J. Chem. Phys. 133 125103
|
[14] |
Wang J, Zhang K, Xu L and Wang E K 2011 Proc. Natl. Acad. Sci.USA 108 8257
|
[15] |
Feng H D and Wang J 2011 J. Chem. Phys. 135 234511
|
[16] |
Feng H D and Wang J 2012 Sci. Rep. 2 550
|
[17] |
Zhang K, Sasai M and Wang J 2013 Proc. Natl. Acad. Sci. USA 11014930
|
[18] |
Li C H and Wang J 2013 PLoS Comput. Biol. 9 e1003165
|
[19] |
Xu L, Zhang K and Wang J 2014 PLoS One 9 e105216
|
[20] |
Gerard C and Goldbeter A 2009 Proc. Natl. Acad. Sci. USA 106 21643
|
[21] |
Gerard C and Goldbeter A 2012 PLoS Comput. Biol. 8 e1002516
|
[22] |
Xu L, Zhang F, Zhang K, Wang E K and Wang J 2014 PLoS ONE 9e86746
|
[23] |
Zhang F, Xu L, Zhang K, Wang E K and Wang J 2012 J. Chem. Phys.137 065102
|
[24] |
Yan H, Zhao L, Hu L, Wang X, Wang E K and Wang J 2013 Proc. Natl.Acad. Sci. USA 110 E4185
|
[25] |
Koretke K K, Luthey-Schulten Z A and Wolynes P G 1998 Proc. Natl.Acad. Sci. USA 95 2932
|
[26] |
Wang J and Verkhivker G M 2003 Phys. Rev. Lett. 90 188101
|
[27] |
Levy Y, Wolynes P G and Onuchic J N 2004 Proc. Natl. Acad. Sci. USA101 511
|
[28] |
Wang J, Zheng X, Yang Y, Drueckhammer D, Yang W, Verkhivker Gand Wang E 2007 Phys. Rev. Lett. 99 198101
|
[29] |
Chu X, Gan L, Wang E and Wang J 2013 Proc. Natl. Acad. Sci. USA110 E2342
|
[30] |
Goldstein R A, Luthey-Schulten Z A and Wolynes P G 1992 Proc. Natl.Acad. Sci. USA 89 4918
|
[31] |
Goldstein R A, Luthey-Schulten Z A and Wolynes P G 1992 Proc. Natl.Acad. Sci. USA 89 9029
|
[32] |
Hardin C, Eastwood M P, Luthey-Schulten Z and Wolynes P G 2000Proc. Natl. Acad. Sci. USA 97 14235
|
[33] |
Takada S 2001 Proteins 42 85
|
[34] |
Fain B and Levitt M 2003 Proc. Natl. Acad. Sci. USA 100 10700
|
[35] |
Liu Z, Dominy B N and Shakhnovich E I 2004 J. Am. Chem. Soc. 1268515
|
[36] |
Yan Z and Wang J 2012 Sci. Rep. 2 309
|
[37] |
Yan Z, Guo L, Hu L and Wang J 2013 Bioinformatics 29 1127
|
[38] |
Yan Z and Wang J 2013 PloS ONE 8 e74443
|
[39] |
Li C H and Wang J 2014 J. R. Soc. Interf. 11 20140774
|
[40] |
Van Kampen N G 2007 Stochastic Processes in Physics and Chemistry(Amsterdam: Elsevier)
|
[41] |
Hu G 1995 Stochastic Force and Nonlinear Systems (Shanghai: Shanghai Science Education)
|
[42] |
Gardiner C W 2004 Handbook of Stochastic Methods: For Physics,Chemistry and the Natural Sciences (Berlin: Springer-Verlag)
|
[43] |
Risken H 1996 The Fokker-Planck Equation: Methods of Solution andApplications (Berlin: Springer-Verlag)
|
[44] |
Levinthal C 1969 Proceedings in Mossbauer Spectroscopy in Biological Systems. Mossbauer Spectroscopy in Biological Systems: Proceedings of a Meeting Held at Allerton House, Monticello, Illinois. p. 22
|
[45] |
Bryngelson J D, Onuchic J N, Socci N D and Wolynes P G 1995 Proteins 21 167
|
[46] |
Leopold P E, Montal M and Onuchic J N 1992 Proc. Natl. Acad. Sci.USA 89 8721
|
[47] |
Wang J, Onuchic J and Wolynes P 1996 Phys. Rev. Lett. 76 4861
|
[48] |
Frauenfelder H, Sligar S G and Wolynes P G 1991 Science 254 1598
|
[49] |
Tsai C J, Kumar S, Ma B Y and Nussinov R 1999 Protein Sci. 8 1181
|
[50] |
Wang J, Xu L and Wang E 2007 Biophys. J. 92 L109
|
[51] |
Oliveberg M and Wolynes P G 2005 Q. Rev. Biophys. 38 245
|
[52] |
Wolynes P G 2005 Philos. T. Roy. Soc. A 363 453
|
[53] |
Wolynes P G 2005 Q. Rev. Biophys. 38 405
|
[54] |
Wang J, Oliveira R J, Chu X, Whitford P C, Chahine J, Han W, WangE, Onuchic J N and Leite V B P 2012 Proc. Natl. Acad. Sci. USA 10915763
|
[55] |
Chu X and Wang J 2014 PLoS Comput. Biol. 10 e1003782
|
[56] |
Wang Y, Chu X, Suo Z, Wang E and Wang J 2012 J. Am. Chem. Soc.134 13755
|
[57] |
Wang J, Lu Q and Lu H P 2006 PLoS Comput. Biol. 2 e78
|
[58] |
Lu Q, Lu P H and Wang J 2007 Phys. Rev. Lett. 98 128105
|
[59] |
Wang J, Wang Y, Chu X, Hagen S J, Han W and Wang E 2011 PLoSComput. Biol. 7 e1001118
|
[60] |
Chu X, Wang Y, Gan L, Bai Y, Han W, Wang E and Wang J 2012 PLoSComput. Biol. 8 e1002608
|
[61] |
Wang Y, Chu X, Longhi S, Roche P, Han W, Wang E and Wang J 2013Proc. Natl. Acad. Sci. USA 110 E3743
|
[62] |
Wang Y, Longhi S, Roche P and Wang J 2014 Proc. Natl. Acad. Sci.USA 111 E1559
|
[63] |
Lu Q and Wang J 2008 J. Am. Chem. Soc. 130 4772
|
[64] |
Lu Q and Wang J 2009 J. Phys. Chem. B 113 1517
|
[65] |
Lai Z Z, Lu Q and Wang J 2011 J. Phys. Chem. B 115 4147
|
[66] |
Wang Y, Tang C, Wang E and Wang J 2012 PLoS Comput. Biol. 8e1002471
|
[67] |
Wang Y, Gan L, Wang E and Wang J 2013 J. Chem. Theory Comput. 984
|
[68] |
Chu X, Liu F, Maxwell B A, Wang Y, Suo Z, Wang H, Han W andWang J 2014 PLoS Comput. Biol. 10 e1003804
|
[69] |
Yan Z Q, Zheng X L, Wang E K and Wang J 2013 Chem. Sci. 4 2387
|
[70] |
Yang Y L, Li G H, Zhao D Y, Yu H Y, Zheng X L, Peng X D, ZhangX E, Fu T, Hu X Q, Niu M S, Ji X F, Zou L B and Wang J 2015 Chem.Sci. 6 2812
|
[71] |
Zheng X and Wang J 2015 PLoS Comput. Biol. 11 e1004212
|
[72] |
Graham R 1989 Macroscopic Potentials, Bifurcations and Noise inDissipative Systems in Noise in Nonlinear Dynamical Systems (Cambridge: Cambridege Unviersity Press)
|
[73] |
Sasai M and Wolynes P G 2003 Proc. Natl. Acad. Sci. USA 100 2374
|
[74] |
Qian H and Reluga T C 2005 Phys. Rev. Lett. 94 028101
|
[75] |
Ao P 2005 Phys. Life Rev. 2 117
|
[76] |
Ao P 2008 Commun. Theor. Phys. 49 1073
|
[77] |
Ao P, Galas D L H and Zhu X 2008 Med Hypotheses 70 678
|
[78] |
Qian H 2014 Phys. Lett. A 378 609
|
[79] |
Feng H D, Han B and Wang J 2011 J. Phys. Chem. B 115 1254
|
[80] |
Li C H, Wang E K and Wang J 2012 J. Chem. Phys. 136 194108
|
[81] |
Wu W and Wang J 2013 J. Phys. Chem. B 117 12908
|
[82] |
Wu W and Wang J 2013 J. Chem. Phys. 139 121920
|
[83] |
Wu W and Wang J 2014 J. Chem. Phys. 141 105104
|
[84] |
Lepzelter D and Wang J 2008 Phys.Rev. E 77 041917
|
[85] |
Kumar S, Bouzida D, Swendsen R H, Kollman P A and Rosenberg J M1992 J. Comput. Chem. 13 1011
|
[86] |
Plotkin S S, Wang J and Wolynes P G 1997 J. Chem. Phys. 106 2932
|
[87] |
Shakhnovich E I 1994 Phys. Rev. Lett. 72 3907
|
[88] |
Iben I E T, Braunstein D, Doster W, Frauenfelder H, Hong M K, Johnson J B, Luck S, Ormos P, Schulte A, Steinbach P J, Xie A H and YoungR D 1989 Phys. Rev. Lett. 62 1916
|
[89] |
Wright P E and Dyson H J 1999 J. Mol. Biol. 293 321
|
[90] |
Dunker A K, Lawson J D, Brown C J, Williams R M, Romero P, Oh J S,Oldfield C J, Campen A M, Ratliff C R, Hipps K W, Ausio J, NissenM S, Reeves R, Kang C H, Kissinger C R, Bailey R W, Griswold M D,Chiu M, Garner E C and Obradovic Z 2001 J. Mol. Graph. Model. 1926
|
[91] |
Tompa P 2002 Trends. Biochem. Sci. 27 527
|
[92] |
Dyson H J and Wright P E 2002 Curr. Opin. Struct. Biol. 12 54
|
[93] |
Wright P E and Dyson H J 2009 Curr. Opin. Struct. Biol. 19 31
|
[94] |
Dunker A K, Garner E, Guilliot S, Romero P, Albrecht K, Hart J,Obradovic Z, Kissinger C and Villafranca J E 1998 Pacific Symposiumon Biocomputing. Pacific Symposium on Biocomputing 473
|
[95] |
Shoemaker B A, Portman J J and Wolynes P G 2000 Proc. Natl. Acad.Sci. USA 97 8868
|
[96] |
Dunker A K, Silman I, Uversky V N and Sussman J L 2008 Curr. Opin.Struct. Biol. 18 756
|
[97] |
Smock R G and Gierasch L M 2009 Science 324 198
|
[98] |
Tantos A, Han K H and Tompa P 2012 Mol. Cell. Endocrinol 348 457
|
[99] |
Clementi C, Nymeyer H and Onuchic J N 2000 J. Mol. Biol. 298 937
|
[100] |
Levy Y, Cho S S, Onuchic J N and Wolynes P G 2005 J. Mol. Biol. 3461121
|
[101] |
Ganguly D, Zhang W and Chen J 2013 PLoS Comput. Biol. 9 e1003363
|
[102] |
Turjanski A G, Gutkind J S, Best R B and Hummer G 2008 PLoS Comput. Biol. 4 2008 PLoS Com-put. Biol. 4 e1000060
|
[103] |
Ganguly D and Chen J 2011 Proteins: Struc. Funct. Bioinform. 791251
|
[104] |
Huang Y and Liu Z 2009 J. Mol. Biol. 393 1143
|
[105] |
Hansen D F, Zhou Z, Fen H Q, Jenkins L M M, Bai Y W and Kay L E2009 J. Mol. Biol. 387 1
|
[106] |
Pappu R V, Mao A H, Crick S L, Vitalis A and Chicoine C L 2010Proc. Natl. Acad. Sci. USA 107 8183
|
[107] |
Muller-Spath S, Soranno A, Hirschfeld V, Hofmann H, Ruegger S,Reymond L, Nettels D and Schuler B 2010 Proc. Natl. Acad. Sci. USA107 14609
|
[108] |
Haran G and England J L 2010 Proc. Natl. Acad. Sci. USA 107 14519
|
[109] |
Shaw D E, Maragakis P, Lindorff-Larsen K, Piana S, Dror R O, Eastwood M P, Bank J A, Jumper J M, Salmon J K, Shan Y, et al. 2010Science 330 341
|
[110] |
Lindorff-Larsen K, Piana S, Dror R O and Shaw D E 2011 Science 334517
|
[111] |
Narayanan R, Ganesh O K, Edison A S and Hagen S J 2008 J. Am.Chem. Soc. 130 11477
|
[112] |
Longhi S, Receveur-Bréchot V, Karlin D, Johansson K, Darbon H, Bhella D, Yeo R, Finet S and Canard B 2003 J. Biol. Chem. 278 18638
|
[113] |
Bourhis J M, Johansson K, Receveur-Bréchot V, Oldfield C J, Dunker ′K A, Canard B and Longhi S 2004 Virus Res. 99 157
|
[114] |
Bourhis J M, Receveur-Bréchot V, Oglesbee M, Zhang X, Buccellato ′M, Darbon H, Canard B, Finet S and Longhi S 2005 Protein Sci. 141975
|
[115] |
Jensen M R, Communie G, Ribeiro E A, Martinez N, Desfosses A,Salmon L, Mollica L, Gabel F, Jamin M, Longhi S et al. 2011 Proc.Natl. Acad. Sci. USA 108 9839
|
[116] |
Piana S, Lindorff-Larsen K and Shaw D E 2011 Biophys. J. 100 L47
|
[117] |
Daura X, Gademann K, Jaun B, Seebach D, van Gunsteren W F andMark A E 1999 Angew. Chem. Int. Ed. 38 236
|
[118] |
Koshland D E 1958 Proc. Natl. Acad. Sci. USA 44 98
|
[119] |
Ma B Y, Kumar S, Tsai C J and Nussinov R 1999 Protein Eng. 12 713
|
[120] |
Boehr D D, Nussinov R and Wright P E 2009 Nat. Chem. Biol. 5 789
|
[121] |
Okazaki K i, Koga N, Takada S, Onuchic J N and Wolynes P G 2006Proc. Natl. Acad. Sci. USA 103 11844
|
[122] |
Okazaki K i and Takada S 2008 Proc. Natl. Acad. Sci. USA 105 11182
|
[123] |
Whitford P C, Miyashita O, Levy Y and Onuchic J N 2007 J. Mol. Biol.366 1661
|
[124] |
Berry M B, Meador B, Bilderback T, Liang P, Glaser M and PhillipsG N 1994 Proteins 19 183
|
[125] |
Berry M B, Bae E, Bilderback T R, Glaser M and Phillips G N 2006Proteins 62 555
|
[126] |
Wong J H, Fiala K A, Suo Z and Ling H 2008 J. Mol. Biol. 379 317
|
[127] |
Ohmori H, Friedberg E, Fuchs R, Goodman M, Hanaoka F, Hinkle D,Kunkel T, Lawrence C, Livneh Z, Nohmi T, Prakash L, Prakash S, TodoT, Walker G, Wang Z and Woodgate R 2001 Mol. Cell 8 7
|
[128] |
Janin J 1995 Biochimie 77 497
|
[129] |
Havranek J J and Harbury P B 2003 Nat. Struct. Mol. Biol. 10 45
|
[130] |
Kortemme T, Joachimiak L A, Bullock A N, Schuler A D, StoddardB L and Baker D 2004 Nat. Struct. Mol. Biol. 11 371
|
[131] |
Bolon D N, Grant R A, Baker T A and Sauer R T 2005 Proc. Natl.Acad. Sci. USA 102 12724
|
[132] |
Liu Z, Zheng X, Yang X, Wang E and Wang J 2009 Biophys. J. 96 3917
|
[133] |
Li D, Liu Z, Zhao W, Zheng X, Wang J and Wang E 2013 Eur. J.Pharm. Sci. 48 658
|
[134] |
Liu Z, Li D, Zhao W, Zheng X, Wang J and Wang E 2012 PLoS ONE7 e37841
|
[135] |
Zhao W, Li D, Liu Z, Zheng X, Wang J and Wang E 2013 PLoS ONE8 e66362
|
[136] |
Zheng X, Liu Z, Li D, Wang E and Wang J 2013 Curr. Pharm. Des. 192246
|
[137] |
Liu Z, Li D, Zheng X, Wang E and Wang J 2013 Curr. Pharm. Des. 192259
|
[138] |
Zheng X, Gan L, Wang E and Wang J 2013 The AAPS. Journal 15 228
|
[139] |
Vauquelin G and Van Liefde I 2006 Trends Pharmacol. Sci. 27 355
|
[140] |
Tummino P J and Copeland R A 2008 Biochemistry 47 5481
|
[141] |
Yan Z, Zheng X, Wang E and Wang J 2013 Chem. Sci. 4 2387
|
[142] |
Socci N D, Onuchic J N and Wolynes P G 1996 J. Chem. Phys. 1045860
|
[143] |
Wang J 2006 Chem. Phys. Lett. 418 544
|
[144] |
Shoichet B K 2004 Nature 432 862
|
[145] |
Swinney D C 2004 Nat. Rev. Drug Discov. 3 801
|
[146] |
Swinney D C 2006 Lett. Drug Des. Discov. 3 569
|
[147] |
Copeland R A, Pompliano D L and Meek T D 2006 Nat. Rev. DrugDiscov. 5 730
|
[148] |
Lu H and Tonge P J 2010 Curr. Opin. Chem. Biol. 14 467
|
[149] |
Xu L F, Shi H L, Feng H D and Wang J 2012 J. Chem. Phys. 136165102
|
[150] |
Xu L, Zhang F, Wang E K and Wang J 2013 Nonlinearity 26 69
|
[151] |
V Blickle T Speck L H U S and Bechinger C 2006 Phys. Rev. Lett. 96070603
|
[152] |
Seifert U 2005 Phys. Rev. Lett. 95 040602
|
[153] |
Seifert U and Speck T 2010 Europhys. Lett. 89 10007
|
[154] |
Speck T and Seifert U 2005 J. Phys. A 38 L581
|
[155] |
Esposito M and Van den Broeck C 2010 Phys. Rev. Lett. 104 090601
|
[156] |
Esposito M and Van den Broeck C 2010 Phys. Rev. E 82 011143
|
[157] |
Esposito M and Van den Broeck C 2010 Phys. Rev. E 82 011144
|
[158] |
Ge H and Qian H 2010 Phys. Rev. E 81 051133
|
[159] |
Singhania R, Sramkoski R M, Jacobberger J W, and Tyson J J 2011PLoS Comput. Biol. 7 e1001077
|
[160] |
Han B and Wang J 2007 Biophys. J. 92 3755
|
[161] |
Waddington C H 1957 The Strategy of the Genes (London: Allen andUnwin)
|
[162] |
Zhang B and Wolynes P G 2014 Proc. Natl. Acad. Sci. USA 111 10185
|
[163] |
Walczak A M, Sasai M and Wolynes P G 2005 Biophys. J. 88 828
|
[164] |
Ferrell J E 2012 Curr. Biol. 22 R458
|
[165] |
Huang S, Guo Y P, May G and Enver T 2007 Dev. Biol. 305 695
|
[166] |
Li C H and Wang J 2013 J. R. Soc. Interf. 10 20130787
|
[167] |
Feng H D, Zhang K and Wang J 2014 Chem. Sci. 5 3761
|
[168] |
Huang S, Ernberg I and Kauffman S 2009 Semin Cell Dev. Biol. 20 869
|
[169] |
Kalmar T, Lim C, Hayward P, Munoz-Descalzo S and Nichols J 2009PLoS Biol. 7
|
[170] |
Singh A M, Hamazaki T, Hankowski K E and Terada N 2007 StemCells 25 2534
|
[171] |
Onsager L and Machlup S 1953 Phys. Rev. 91 1505
|
[172] |
Hunt K L C and Ross J 1981 J. Chem. Phys. 75 976
|
[173] |
Kramers H A 1940 Physica 7 284
|
[174] |
Maier R S and Stein D L 1997 SIAM J. Appl. Math. 57 752
|
[175] |
Hanggi P, Talkner P and Borkovec M ¨ 1990 Rev. Mod. Phys. 62 251
|
[176] |
Weinberg R A 2013 The Biology of Cancer (New York: Taylor & Francis)
|
[177] |
Hanahan D and Weinberg R A 2011 Cell 144 646
|
[178] |
Hanahan D and Weinberg R A 2000 Cell 100 57
|
[179] |
Kauffman S 1971 J. Theor. Biol. 31 429
|
[180] |
Lu M, Onuchic J N and Ben-Jacob E 2014 Phys. Rev. Lett. 113 078102
|
[181] |
Lu M, Jolly M K, Gomoto R, Huang B, Onuchic J N and Ben-Jacob E2013 J. Phys. Chem. B 117 13164
|
[182] |
Lu M, Jolly M K, Levine H, Onuchic J N and Ben-Jacob E 2013 Proc.Natl. Acad. Sci. USA 110 18144
|
[183] |
Jolly M K, Huang B, Lu M, Mani S A, Levine H and Ben-Jacob E 2014J. R. Soc. Interface 11 20140962
|
[184] |
Wright S 1932 Proceedings of the Sixth International Congress on Genetics 1 356
|
[185] |
Fisher R A 1930 The Genetical Theory of Natural Selection (NewYork: Clarendon and Oxford)
|
[186] |
Rice S H 2004 Evolutionary Theory: Mathematical and ConceptualFoundations (Sinauer Associates)
|
[187] |
Van Valen L 1973 Evol Theory 1 1
|
[188] |
Murray J 1998 Mathematical Biology (New York/Berlin: Springer)
|
[189] |
Lotka A 1925 Elements of Physical Biology (Baltimore: Williams andWilkins)
|
[190] |
Volterra V 1931 Lecons sur la Theorie Mathematique de la Lutte pourla Vie (Paris: Gauthier-Villars)
|
[191] |
Goh B 1976 J. Math. Biol. 3 313
|
[192] |
Hastings A 1977 J. Math. Biol. 5 399
|
[193] |
Bazykin A 1985 Mathematical Biophysics of Interacting Populations(Moscow: Nauka) (in Russian)
|
[194] |
Abbott L F and Regehr W G 2004 Nature 431 796
|
[195] |
Abbott L F 2008 Neuron 60 489
|
[196] |
Vogels T P, Rajan K and Abbott L F 2005 Annu. Rev. Neurosci. 28 357
|
[197] |
Hodgkin A L and Huxley A F 1952 J. Physiol. 117 500
|
[198] |
Hopfield J J 1982 Proc.Natl. Acad. Sci. USA 79 2554
|
[199] |
Hopfield J J and Tank D W 1986 Science 233 625
|
[200] |
Arnsten A F T, Wang M, Gamo N J, Yang Y, Jin L E, Wang X J,Laubach M, Mazer J A and Lee D 2011 Nature 476 210
|
[201] |
Buzsaki G and Draguhn A 2004 Science 304 1926
|
[202] |
Wang X J, Tegner J, Constantinidis C and Goldman-Rakic P S 2004Proc. Natl. Acad. Sci. USA 101 1368
|
[203] |
McCarley R W and Massaquoi S G 1986 Am. J. Physiol-Reg. I 251R1011
|
[204] |
Massaquoi S G and McCarley R W 1992 J. Sleep. Res. 1 138
|