-
7
-
-
70349252618
-
Theory of RNA Folding: From Hairpins to Ribozymes
-
Walter, N. Woodson, S. Batey, R. Springer: Berlin, Vol
-
Thirumalai, D.; Hyeon, C. Theory of RNA Folding: From Hairpins to Ribozymes. In Non-Protein Coding RNAs; Walter, N.; Woodson, S.; Batey, R., Eds.; Springer: Berlin, 2009; Vol. 13, pp 27-47.
-
(2009)
Non-Protein Coding RNAs
, vol.13
, pp. 27-47
-
-
Thirumalai, D.1
Hyeon, C.2
-
9
-
-
0031285905
-
-
Thirumalai, D.; Klimov, D. K.; Woodson, S. A. Theor. Chem. Acc. 1997, 96, 14-22
-
(1997)
Theor. Chem. Acc.
, vol.96
, pp. 14-22
-
-
Thirumalai, D.1
Klimov, D.K.2
Woodson, S.A.3
-
10
-
-
84870802321
-
-
Lin, J. C.; Hyeon, C.; Thirumalai, D. J. Phys. Chem. Lett. 2012, 3, 3616-3625
-
(2012)
J. Phys. Chem. Lett.
, vol.3
, pp. 3616-3625
-
-
Lin, J.C.1
Hyeon, C.2
Thirumalai, D.3
-
11
-
-
0034743153
-
-
Thirumalai, D.; Lee, N.; Woodson, S. A.; Klimov, D. K. Annu. Rev. Phys. Chem. 2001, 52, 751-762
-
(2001)
Annu. Rev. Phys. Chem.
, vol.52
, pp. 751-762
-
-
Thirumalai, D.1
Lee, N.2
Woodson, S.A.3
Klimov, D.K.4
-
14
-
-
32244445917
-
-
Ma, H.; Proctor, D. J.; Kierzek, E.; Kierzek, R.; Bevilacqua, P. C.; Gruebele, M. J. Am. Chem. Soc. 2006, 128, 1523-1530
-
(2006)
J. Am. Chem. Soc.
, vol.128
, pp. 1523-1530
-
-
Ma, H.1
Proctor, D.J.2
Kierzek, E.3
Kierzek, R.4
Bevilacqua, P.C.5
Gruebele, M.6
-
16
-
-
33846468971
-
-
Ma, H.; Wan, C.; Wu, A.; Zewail, A. H. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 712-716
-
(2007)
Proc. Natl. Acad. Sci. U.S.A.
, vol.104
, pp. 712-716
-
-
Ma, H.1
Wan, C.2
Wu, A.3
Zewail, A.H.4
-
19
-
-
84875989318
-
-
Kührová, P.; Banás, P.; Best, R. B.; Sponer, J.; Otyepka, M. J. Chem. Theory Comput. 2013, 9, 2115-2125
-
(2013)
J. Chem. Theory Comput.
, vol.9
, pp. 2115-2125
-
-
Kührová, P.1
Banás, P.2
Best, R.B.3
Sponer, J.4
Otyepka, M.5
-
20
-
-
0042797442
-
-
Cambridge University Press: Cambridge, U.K
-
Wales, D. J. Energy Landscapes; Cambridge University Press: Cambridge, U.K., 2003.
-
(2003)
Energy Landscapes
-
-
Wales, D.J.1
-
22
-
-
0000672766
-
-
Doye, J. P. K.; Miller, M. A.; Wales, D. J. J. Chem. Phys. 1999, 110, 6896-6906
-
(1999)
J. Chem. Phys.
, vol.110
, pp. 6896-6906
-
-
Doye, J.P.K.1
Miller, M.A.2
Wales, D.J.3
-
24
-
-
0025047647
-
-
Woese, C. R.; Winker, S.; Gutell, R. R. Proc. Natl. Acad. Sci. U.S.A. 1990, 87, 8467-8471
-
(1990)
Proc. Natl. Acad. Sci. U.S.A.
, vol.87
, pp. 8467-8471
-
-
Woese, C.R.1
Winker, S.2
Gutell, R.R.3
-
26
-
-
0029001288
-
-
Marino, J. P.; Gregorian, J.; Razmic, S.; Csankovszki, G.; Crothers, D. M. Science 1995, 268, 1448-1454
-
(1995)
Science
, vol.268
, pp. 1448-1454
-
-
Marino, J.P.1
Gregorian, J.2
Razmic, S.3
Csankovszki, G.4
Crothers, D.M.5
-
28
-
-
0028294458
-
-
Jaeger, L.; Michel, F.; Westhof, E. J. Mol. Biol. 1994, 236, 1271-1276
-
(1994)
J. Mol. Biol.
, vol.236
, pp. 1271-1276
-
-
Jaeger, L.1
Michel, F.2
Westhof, E.3
-
30
-
-
84890281265
-
-
Thapar, R.; Denmon, A. P.; Nikonowicz, E. P. Wiley Interdiscip. Rev.: RNA 2014, 5, 49-67
-
(2014)
Wiley Interdiscip. Rev.: RNA
, vol.5
, pp. 49-67
-
-
Thapar, R.1
Denmon, A.P.2
Nikonowicz, E.P.3
-
31
-
-
0030596092
-
-
Jucker, F. M.; Heus, H. A.; Yip, P. F.; Moors, E. H. M.; Pardi, A. J. Mol. Biol. 1996, 264, 968-980
-
(1996)
J. Mol. Biol.
, vol.264
, pp. 968-980
-
-
Jucker, F.M.1
Heus, H.A.2
Yip, P.F.3
Moors, E.H.M.4
Pardi, A.5
-
32
-
-
75149139054
-
-
Sheehy, J. P.; Davis, A. R.; Znosko, B. M. RNA 2010, 16, 417-429
-
(2010)
RNA
, vol.16
, pp. 417-429
-
-
Sheehy, J.P.1
Davis, A.R.2
Znosko, B.M.3
-
34
-
-
0032555119
-
-
Bonnet, G.; Krichevsky, O.; Libchaber, A. Proc. Natl. Acad. Sci. U.S.A. 1998, 95, 8602-8606
-
(1998)
Proc. Natl. Acad. Sci. U.S.A.
, vol.95
, pp. 8602-8606
-
-
Bonnet, G.1
Krichevsky, O.2
Libchaber, A.3
-
35
-
-
0000060975
-
-
Ying, L.; Wallace, M. I.; Klenerman, D. Chem. Phys. Lett. 2001, 334, 145-150
-
(2001)
Chem. Phys. Lett.
, vol.334
, pp. 145-150
-
-
Ying, L.1
Wallace, M.I.2
Klenerman, D.3
-
36
-
-
0034934258
-
-
Ansari, A.; Kuznetsov, S. V.; Shen, Y. Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 7771-7776
-
(2001)
Proc. Natl. Acad. Sci. U.S.A.
, vol.98
, pp. 7771-7776
-
-
Ansari, A.1
Kuznetsov, S.V.2
Shen, Y.3
-
37
-
-
70349594633
-
-
Sarkar, K.; Meister, K.; Sethi, A.; Gruebele, M. Biophys. J. 2009, 97, 1418-1427
-
(2009)
Biophys. J.
, vol.97
, pp. 1418-1427
-
-
Sarkar, K.1
Meister, K.2
Sethi, A.3
Gruebele, M.4
-
38
-
-
78649649131
-
-
Sarkar, K.; Nguyen, D. A.; Gruebele, M. RNA 2010, 16, 2427-2434
-
(2010)
RNA
, vol.16
, pp. 2427-2434
-
-
Sarkar, K.1
Nguyen, D.A.2
Gruebele, M.3
-
40
-
-
33744502886
-
-
Kim, J.; Doose, S.; Neuweiler, H.; Sauer, M. Nucleic Acids Res. 2006, 34, 2516-2527
-
(2006)
Nucleic Acids Res.
, vol.34
, pp. 2516-2527
-
-
Kim, J.1
Doose, S.2
Neuweiler, H.3
Sauer, M.4
-
41
-
-
84869455755
-
-
Narayanan, R.; Zhu, L.; Velmurugu, Y.; Roca, J.; Kuznetsov, S. V.; Prehna, G.; Lapidus, L. J.; Ansari, A. J. Am. Chem. Soc. 2012, 134, 18952-18963
-
(2012)
J. Am. Chem. Soc.
, vol.134
, pp. 18952-18963
-
-
Narayanan, R.1
Zhu, L.2
Velmurugu, Y.3
Roca, J.4
Kuznetsov, S.V.5
Prehna, G.6
Lapidus, L.J.7
Ansari, A.8
-
43
-
-
0042845840
-
-
Sorin, E. J.; Rhee, Y. M.; Pande, V. S. Biophys. J. 2003, 85, 790-803
-
(2003)
Biophys. J.
, vol.85
, pp. 790-803
-
-
Sorin, E.J.1
Rhee, Y.M.2
Pande, V.S.3
-
44
-
-
22144496413
-
-
Sorin, E. J.; Rhee, Y. M.; Pande, V. S. Biophys. J. 2005, 88, 2516-2524
-
(2005)
Biophys. J.
, vol.88
, pp. 2516-2524
-
-
Sorin, E.J.1
Rhee, Y.M.2
Pande, V.S.3
-
46
-
-
36749052211
-
-
Zhuang, Z.; Jaeger, L.; Shea, J. E. Nucleic Acids Res. 2007, 35, 6995-7002
-
(2007)
Nucleic Acids Res.
, vol.35
, pp. 6995-7002
-
-
Zhuang, Z.1
Jaeger, L.2
Shea, J.E.3
-
47
-
-
77951809910
-
-
Zuo, G.; Li, W.; Zhang, J.; Wang, J.; Wang, W. J. Phys. Chem. B 2010, 114, 5835-5839
-
(2010)
J. Phys. Chem. B
, vol.114
, pp. 5835-5839
-
-
Zuo, G.1
Li, W.2
Zhang, J.3
Wang, J.4
Wang, W.5
-
48
-
-
48249117491
-
-
Bowman, G. R.; Huang, X.; Yao, Y.; Sun, J.; Carlsson, G.; Guibas, L. J.; Pande, V. S. J. Am. Chem. Soc. 2008, 130, 9676-9678
-
(2008)
J. Am. Chem. Soc.
, vol.130
, pp. 9676-9678
-
-
Bowman, G.R.1
Huang, X.2
Yao, Y.3
Sun, J.4
Carlsson, G.5
Guibas, L.J.6
Pande, V.S.7
-
49
-
-
65249153026
-
-
Yao, Y.; Sun, J.; Huang, X.; Bowman, G. R.; Singh, G.; Lesnick, M.; Pande, V. S.; Guibas, L. J.; Carlsson, G. J. Chem. Phys. 2009, 130, 144115-1-14115-10
-
(2009)
J. Chem. Phys.
, vol.130
, pp. 1441151-1411510
-
-
Yao, Y.1
Sun, J.2
Huang, X.3
Bowman, G.R.4
Singh, G.5
Lesnick, M.6
Pande, V.S.7
Guibas, L.J.8
Carlsson, G.9
-
50
-
-
47649132118
-
-
Lin, M. M.; Meinhold, L.; Shorokov, L.; Zewail, A. H. Phys. Chem. Chem. Phys. 2008, 10, 4227-4239
-
(2008)
Phys. Chem. Chem. Phys.
, vol.10
, pp. 4227-4239
-
-
Lin, M.M.1
Meinhold, L.2
Shorokov, L.3
Zewail, A.H.4
-
51
-
-
38649086360
-
-
Villa, A.; Widjajakusuma, E.; Stock, G. J. Phys. Chem. B 2008, 112, 134-142
-
(2008)
J. Phys. Chem. B
, vol.112
, pp. 134-142
-
-
Villa, A.1
Widjajakusuma, E.2
Stock, G.3
-
53
-
-
0036297661
-
-
Sorin, E. J.; Engelhardt, M. A.; Herschlag, D.; Pande, V. S. J. Mol. Biol. 2002, 317, 493-506
-
(2002)
J. Mol. Biol.
, vol.317
, pp. 493-506
-
-
Sorin, E.J.1
Engelhardt, M.A.2
Herschlag, D.3
Pande, V.S.4
-
65
-
-
0037145606
-
-
Wales, D. J. Mol. Phys. 2002, 100, 3285-3305
-
(2002)
Mol. Phys.
, vol.100
, pp. 3285-3305
-
-
Wales, D.J.1
-
69
-
-
66749117149
-
-
Wales, D. J. J. Chem. Phys. 2009, 130, 204111(1)-204111(7)
-
(2009)
J. Chem. Phys.
, vol.130
, pp. 2041111-2041117
-
-
Wales, D.J.1
-
70
-
-
8344253719
-
-
Proctor, D. J.; Ma, H.; Kierzek, E.; Kierzek, R.; Gruebele, M.; Bevilacqua, P. C. Biochemistry 2004, 43, 14004-14014
-
(2004)
Biochemistry
, vol.43
, pp. 14004-14014
-
-
Proctor, D.J.1
Ma, H.2
Kierzek, E.3
Kierzek, R.4
Gruebele, M.5
Bevilacqua, P.C.6
-
71
-
-
0034680628
-
-
Ennifar, E.; Nikulin, A.; Tishchenko, S.; Serganov, A.; Nevskaya, N.; Garber, M.; Ehresmann, B.; Ehresmann, C.; Nikonov, S.; Dumas, P. J. Mol. Biol. 2000, 304, 35-42
-
(2000)
J. Mol. Biol.
, vol.304
, pp. 35-42
-
-
Ennifar, E.1
Nikulin, A.2
Tishchenko, S.3
Serganov, A.4
Nevskaya, N.5
Garber, M.6
Ehresmann, B.7
Ehresmann, C.8
Nikonov, S.9
Dumas, P.10
-
72
-
-
0030596092
-
-
Jucker, F. M.; Heus, H. A.; Yip, P. F.; Moors, E. H. M.; Pardi, A. J. Mol. Biol. 1996, 264, 968-980
-
(1996)
J. Mol. Biol.
, vol.264
, pp. 968-980
-
-
Jucker, F.M.1
Heus, H.A.2
Yip, P.F.3
Moors, E.H.M.4
Pardi, A.5
-
74
-
-
77950907056
-
-
Malolepsza, E.; Strodel, B.; Khalili, M.; Trygubenko, S.; Fejer, S. N.; Wales, D. J. J. Comput. Chem. 2010, 31, 1402-1409
-
(2010)
J. Comput. Chem.
, vol.31
, pp. 1402-1409
-
-
Malolepsza, E.1
Strodel, B.2
Khalili, M.3
Trygubenko, S.4
Fejer, S.N.5
Wales, D.J.6
-
75
-
-
34250318638
-
-
Pérez, A.; Marchán, I.; Svozil, D.; Sponer, J.; Cheatham, T. E.; Laughton, C. A.; Orozco, M. Biophys. J. 2007, 92, 3817-3829
-
(2007)
Biophys. J.
, vol.92
, pp. 3817-3829
-
-
Pérez, A.1
Marchán, I.2
Svozil, D.3
Sponer, J.4
Cheatham, T.E.5
Laughton, C.A.6
Orozco, M.7
-
76
-
-
80052820313
-
-
Zgarbová, M.; Otyepka, M.; Sponer, J.; Mládek, A.; Banás, P.; Cheatham, T. E.; Jurecka, P. J. Chem. Theory Comput. 2011, 7, 2886-2902
-
(2011)
J. Chem. Theory Comput.
, vol.7
, pp. 2886-2902
-
-
Zgarbová, M.1
Otyepka, M.2
Sponer, J.3
Mládek, A.4
Banás, P.5
Cheatham, T.E.6
Jurecka, P.7
-
77
-
-
1842479952
-
-
Onufriev, A.; Bashford, D.; Case, D. A. Proteins 2004, 55, 383-394
-
(2004)
Proteins
, vol.55
, pp. 383-394
-
-
Onufriev, A.1
Bashford, D.2
Case, D.A.3
-
78
-
-
20644449471
-
-
Onufriev, A.; Bashford, D.; Case, D. A. J. Phys. Chem. B 2000, 104, 3712-3720
-
(2000)
J. Phys. Chem. B
, vol.104
, pp. 3712-3720
-
-
Onufriev, A.1
Bashford, D.2
Case, D.A.3
-
79
-
-
0033468737
-
-
Srinivasan, J.; Trevathan, M. W.; Beroza, P.; Case, D. A. Theor. Chem. Acc. 1999, 101, 426-434
-
(1999)
Theor. Chem. Acc.
, vol.101
, pp. 426-434
-
-
Srinivasan, J.1
Trevathan, M.W.2
Beroza, P.3
Case, D.A.4
-
80
-
-
84930935984
-
-
Case, D. A.; Darden, T. A.; Cheatham, T.; Simmerling, C. L.; Wang, J.; Duke, R. E.; Luo, R.; Walker, R. C.; Zhang, W.; Merz, K. M.; Roberts, B.; Hayik, S.; Roitberg, A.; Seabra, G.; Swails, J.; Goetz, A. W.; Kolossváry, I. AMBER 12; 2012. http://ambermd.org/.
-
(2012)
AMBER
, vol.12
-
-
Case, D.A.1
Darden, T.A.2
Cheatham, T.3
Simmerling, C.L.4
Wang, J.5
Duke, R.E.6
Luo, R.7
Walker, R.C.8
Zhang, W.9
Merz, K.M.10
Roberts, B.11
Hayik, S.12
Roitberg, A.13
Seabra, G.14
Swails, J.15
Goetz, A.W.16
Kolossváry, I.17
-
81
-
-
0026869597
-
-
Loncharich, R. J.; Brooks, B. R.; Pastor, R. W. Biopolymers 1992, 32, 523-535
-
(1992)
Biopolymers
, vol.32
, pp. 523-535
-
-
Loncharich, R.J.1
Brooks, B.R.2
Pastor, R.W.3
-
84
-
-
84878126193
-
-
Farrell, J. D.; Lines, C.; Shepherd, J. J.; Chakrabarti, D.; Miller, M. A.; Wales, D. J. Soft Matter 2013, 9, 5407-5416
-
(2013)
Soft Matter
, vol.9
, pp. 5407-5416
-
-
Farrell, J.D.1
Lines, C.2
Shepherd, J.J.3
Chakrabarti, D.4
Miller, M.A.5
Wales, D.J.6
-
89
-
-
0034513054
-
-
Henkelman, G.; Uberuaga, B. P.; Jonsson, H. J. Chem. Phys. 2000, 113, 9901-9904
-
(2000)
J. Chem. Phys.
, vol.113
, pp. 9901-9904
-
-
Henkelman, G.1
Uberuaga, B.P.2
Jonsson, H.3
-
92
-
-
84920124484
-
-
Case, D. A.; Darden, T. A.; Cheatham, T.; Simmerling, C. L.; Wang, J.; Duke, R. E.; Luo, R.; Walker, R. C.; Zhang, W.; Merz, K. M.; Roberts, B.; Hayik, S.; Roitberg, A.; Seabra, G.; Swails, J.; Goetz, A. W.; Kolossváry, I. AMBER 9; 2006. http://ambermd.org/.
-
(2006)
AMBER
, vol.9
-
-
Case, D.A.1
Darden, T.A.2
Cheatham, T.3
Simmerling, C.L.4
Wang, J.5
Duke, R.E.6
Luo, R.7
Walker, R.C.8
Zhang, W.9
Merz, K.M.10
Roberts, B.11
Hayik, S.12
Roitberg, A.13
Seabra, G.14
Swails, J.15
Goetz, A.W.16
Kolossváry, I.17
-
93
-
-
37549055108
-
-
Strodel, B.; Whittleston, C. W.; Wales, D. J. J. Am. Chem. Soc. 2007, 129, 16005-16014
-
(2007)
J. Am. Chem. Soc.
, vol.129
, pp. 16005-16014
-
-
Strodel, B.1
Whittleston, C.W.2
Wales, D.J.3
-
96
-
-
84967520812
-
-
Connerade, J. P. Solov'yov, A. Imperial College Press: London
-
Carr, J. M.; Wales, D. J. In The Energy Landscape as a Computational Tool; Connerade, J. P.; Solov'yov, A., Eds.; Imperial College Press: London, 2008; pp 321-330.
-
(2008)
The Energy Landscape As A Computational Tool
, pp. 321-330
-
-
Carr, J.M.1
Wales, D.J.2
-
97
-
-
2142678730
-
-
Springer: Berlin
-
Jimenez, J.; Marzal, A. In Algorithm Engineering: 3rd International Workshop, WAE'99, London, UK, July 1999; Springer: Berlin, 1999; pp 15-29.
-
(1999)
Algorithm Engineering: 3rd International Workshop, WAE'99, London, UK, July 1999
, pp. 15-29
-
-
Jimenez, J.1
Marzal, A.2
-
100
-
-
0001968287
-
-
John Wiley and Sons: New York
-
Hoare, M. R. In Advances in Chemical Physics; John Wiley and Sons: New York, 1979; Vol. 40, pp 49-129.
-
(1979)
Advances in Chemical Physics
, vol.40
, pp. 49-129
-
-
Hoare, M.R.1
-
106
-
-
0032552138
-
-
Wales, D. J.; Miller, M. A.; Walsh, T. R. Nature 1998, 394, 758-760
-
(1998)
Nature
, vol.394
, pp. 758-760
-
-
Wales, D.J.1
Miller, M.A.2
Walsh, T.R.3
-
108
-
-
77955817276
-
-
DePaul, A. J.; Thompson, E. J.; Patel, S. S.; Haideman, K.; Sorin, E. J. Nucleic Acids Res. 2010, 4856-4867
-
(2010)
Nucleic Acids Res.
, pp. 4856-4867
-
-
Depaul, A.J.1
Thompson, E.J.2
Patel, S.S.3
Haideman, K.4
Sorin, E.J.5
-
109
-
-
65249110385
-
-
Zhang, Y.; Zhao, X.; Mu, Y. J. Chem. Theory Comput. 2009, 5, 1146-1154
-
(2009)
J. Chem. Theory Comput.
, vol.5
, pp. 1146-1154
-
-
Zhang, Y.1
Zhao, X.2
Mu, Y.3
-
111
-
-
0344119523
-
-
Sarzynska, J.; Nilsson, L.; Kullinski, T. Biophys. J. 2003, 85, 3445-3459
-
(2003)
Biophys. J.
, vol.85
, pp. 3445-3459
-
-
Sarzynska, J.1
Nilsson, L.2
Kullinski, T.3
-
114
-
-
78249249624
-
-
Portella, G.; Orozco, M. Angew. Chem., Int. Ed. 2010, 49, 7673-7676
-
(2010)
Angew. Chem., Int. Ed.
, vol.49
, pp. 7673-7676
-
-
Portella, G.1
Orozco, M.2
-
116
-
-
83755161838
-
-
Biyun, S.; Cho, S. S.; Thirumalai, D. J. Am. Chem. Soc. 2011, 133, 20634-20643
-
(2011)
J. Am. Chem. Soc.
, vol.133
, pp. 20634-20643
-
-
Biyun, S.1
Cho, S.S.2
Thirumalai, D.3
-
117
-
-
84863686749
-
-
Banás, P.; Mládek, A.; Otyepka, M.; Zgarbová, M.; Juercka, P.; Svozil, D.; Lankas, F.; Sponer, J. J. Chem. Theory Comput. 2012, 8, 2448-2460
-
(2012)
J. Chem. Theory Comput.
, vol.8
, pp. 2448-2460
-
-
Banás, P.1
Mládek, A.2
Otyepka, M.3
Zgarbová, M.4
Juercka, P.5
Svozil, D.6
Lankas, F.7
Sponer, J.8
-
119
-
-
84873038722
-
-
Huang, X.; Yao, Y.; Bowman, G. R.; Sun, J.; Guibas, L. J.; Carlsson, G.; Pande, V. S. Pac. Symp. Biocomput. 2010, 15, 228-239
-
(2010)
Pac. Symp. Biocomput.
, vol.15
, pp. 228-239
-
-
Huang, X.1
Yao, Y.2
Bowman, G.R.3
Sun, J.4
Guibas, L.J.5
Carlsson, G.6
Pande, V.S.7
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