-
1
-
-
30344484542
-
-
10.1016/j.jmb.2005.11.058
-
E. J. Sorin, Y. M. Rhee, M. R. Shirts, and V. S. Pande, J. Mol. Biol. 356, 248-256 (2006). 10.1016/j.jmb.2005.11.058
-
(2006)
J. Mol. Biol.
, vol.356
, pp. 248-256
-
-
Sorin, E.J.1
Rhee, Y.M.2
Shirts, M.R.3
Pande, V.S.4
-
2
-
-
0030466444
-
-
10.1016/S1074-5521(96)90164-7
-
J. E. Ladbury, Chem. Biol. 3, 973-980 (1996). 10.1016/S1074-5521(96) 90164-7
-
(1996)
Chem. Biol.
, vol.3
, pp. 973-980
-
-
Ladbury, J.E.1
-
7
-
-
0023779259
-
-
10.1002/prot.340040104
-
M. K. Gilson and B. Honig, Proteins 4, 7-18 (1988). 10.1002/prot. 340040104
-
(1988)
Proteins
, vol.4
, pp. 7-18
-
-
Gilson, M.K.1
Honig, B.2
-
8
-
-
84870807799
-
-
10.1017/S003358351200011X
-
P. Y. Ren, J. H. Chun, D. G. Thomas, M. J. Schnieders, M. Marucho, J. J. Zhang, and N. A. Baker, Q. Rev. Biophys. 45, 427-491 (2012). 10.1017/S003358351200011X
-
(2012)
Q. Rev. Biophys.
, vol.45
, pp. 427-491
-
-
Ren, P.Y.1
Chun, J.H.2
Thomas, D.G.3
Schnieders, M.J.4
Marucho, M.5
Zhang, J.J.6
Baker, N.A.7
-
11
-
-
0029066848
-
-
10.1016/0959-440X(95)80079-4
-
M. K. Gilson, Curr. Opin. Struct. Biol. 5, 216-223 (1995). 10.1016/0959-440X(95)80079-4
-
(1995)
Curr. Opin. Struct. Biol.
, vol.5
, pp. 216-223
-
-
Gilson, M.K.1
-
13
-
-
0035964342
-
-
10.1073/pnas.181342398
-
N. A. Baker, D. Sept, S. Joseph, M. J. Holst, and J. A. McCammon, Proc. Natl. Acad. Sci. U.S.A. 98, 10037-10041 (2001). 10.1073/pnas.181342398
-
(2001)
Proc. Natl. Acad. Sci. U.S.A.
, vol.98
, pp. 10037-10041
-
-
Baker, N.A.1
Sept, D.2
Joseph, S.3
Holst, M.J.4
McCammon, J.A.5
-
16
-
-
0344778061
-
-
10.1021/ja00172a038
-
W. C. Still, A. Tempczyk, R. C. Hawley, and T. Hendrickson, J. Am. Chem. Soc. 112, 6127-6129 (1990). 10.1021/ja00172a038
-
(1990)
J. Am. Chem. Soc.
, vol.112
, pp. 6127-6129
-
-
Still, W.C.1
Tempczyk, A.2
Hawley, R.C.3
Hendrickson, T.4
-
27
-
-
65249187748
-
-
10.1021/ct800409d
-
D. L. Mobley, C. I. Bayly, M. D. Cooper, M. R. Shirts, and K. A. Dill, J. Chem. Theory Comput. 5, 350-358 (2009). 10.1021/ct800409d
-
(2009)
J. Chem. Theory Comput.
, vol.5
, pp. 350-358
-
-
Mobley, D.L.1
Bayly, C.I.2
Cooper, M.D.3
Shirts, M.R.4
Dill, K.A.5
-
28
-
-
33947397110
-
-
10.1021/jp0667442
-
D. L. Mobley, E. Dumont, J. D. Chodera, and K. A. Dill, J. Phys. Chem. B 111, 2242-2254 (2007). 10.1021/jp0667442
-
(2007)
J. Phys. Chem. B
, vol.111
, pp. 2242-2254
-
-
Mobley, D.L.1
Dumont, E.2
Chodera, J.D.3
Dill, K.A.4
-
30
-
-
84863090241
-
-
10.1007/s10822-012-9554-1
-
H. S. Muddana, C. D. Varnado, C. W. Bielawski, A. R. Urbach, L. Isaacs, M. T. Geballe, and M. K. Gilson, J. Comput.-Aided Mol. Des. 26, 475-487 (2012). 10.1007/s10822-012-9554-1
-
(2012)
J. Comput.-Aided Mol. Des.
, vol.26
, pp. 475-487
-
-
Muddana, H.S.1
Varnado, C.D.2
Bielawski, C.W.3
Urbach, A.R.4
Isaacs, L.5
Geballe, M.T.6
Gilson, M.K.7
-
32
-
-
27844560576
-
-
10.1021/ja055013x
-
S. Liu, C. Ruspic, P. Mukhopadhyay, S. Chakrabarti, P. Y. Zavalij, and L. Isaacs, J. Am. Chem. Soc. 127, 15959-15967 (2005). 10.1021/ja055013x
-
(2005)
J. Am. Chem. Soc.
, vol.127
, pp. 15959-15967
-
-
Liu, S.1
Ruspic, C.2
Mukhopadhyay, P.3
Chakrabarti, S.4
Zavalij, P.Y.5
Isaacs, L.6
-
33
-
-
38049144318
-
-
10.1073/pnas.0706407105
-
M. V. Rekharsky, T. Mori, C. Yang, Y. H. Ko, N. Selvapalam, H. Kim, D. Sobransingh, A. E. Kaifer, S. Liu, L. Isaacs, W. Chen, S. Moghaddam, M. K. Gilson, K. Kim, and Y. Inoue, Proc. Natl. Acad. Sci. U.S.A. 104, 20737-20742 (2007). 10.1073/pnas.0706407105
-
(2007)
Proc. Natl. Acad. Sci. U.S.A.
, vol.104
, pp. 20737-20742
-
-
Rekharsky, M.V.1
Mori, T.2
Yang, C.3
Ko, Y.H.4
Selvapalam, N.5
Kim, H.6
Sobransingh, D.7
Kaifer, A.E.8
Liu, S.9
Isaacs, L.10
Chen, W.11
Moghaddam, S.12
Gilson, M.K.13
Kim, K.14
Inoue, Y.15
-
34
-
-
79952586541
-
-
10.1021/ja109904u
-
S. Moghaddam, C. Yang, M. Rekharsky, Y. H. Ko, K. Kim, Y. Inoue, and M. K. Gilson, J. Am. Chem. Soc. 133, 3570-3581 (2011). 10.1021/ja109904u
-
(2011)
J. Am. Chem. Soc.
, vol.133
, pp. 3570-3581
-
-
Moghaddam, S.1
Yang, C.2
Rekharsky, M.3
Ko, Y.H.4
Kim, K.5
Inoue, Y.6
Gilson, M.K.7
-
35
-
-
0001752768
-
-
10.1107/S0108768102003890
-
F. H. Allen, Acta Crystallogr. B 58, 380-388 (2002). 10.1107/ S0108768102003890
-
(2002)
Acta Crystallogr. B
, vol.58
, pp. 380-388
-
-
Allen, F.H.1
-
36
-
-
67849104638
-
-
10.1093/nar/gkp456
-
Y. L. Wang, J. W. Xiao, T. O. Suzek, J. Zhang, J. Y. Wang, and S. H. Bryant, Nucleic Acids Res. 37, W623-W633 (2009). 10.1093/nar/gkp456
-
(2009)
Nucleic Acids Res.
, vol.37
-
-
Wang, Y.L.1
Xiao, J.W.2
Suzek, T.O.3
Zhang, J.4
Wang, J.Y.5
Bryant, S.H.6
-
37
-
-
67849101722
-
-
10.1021/ct9000922
-
J. Rezac, J. Fanfrlik, D. Salahub, and P. Hobza, J. Chem. Theory Comput. 5, 1749-1760 (2009). 10.1021/ct9000922
-
(2009)
J. Chem. Theory Comput.
, vol.5
, pp. 1749-1760
-
-
Rezac, J.1
Fanfrlik, J.2
Salahub, D.3
Hobza, P.4
-
38
-
-
78651286289
-
-
10.1021/ct100408b
-
M. Korth, J. Chem. Theory Comput. 6, 3808-3816 (2010). 10.1021/ct100408b
-
(2010)
J. Chem. Theory Comput.
, vol.6
, pp. 3808-3816
-
-
Korth, M.1
-
40
-
-
25144517646
-
-
10.1002/jcc.20292
-
J. L. Banks, H. S. Beard, Y. X. Cao, A. E. Cho, W. Damm, R. Farid, A. K. Felts, T. A. Halgren, D. T. Mainz, J. R. Maple, R. Murphy, D. M. Philipp, M. P. Repasky, L. Y. Zhang, B. J. Berne, R. A. Friesner, E. Gallicchio, and R. M. Levy, J. Comput. Chem. 26, 1752-1780 (2005). 10.1002/jcc.20292
-
(2005)
J. Comput. Chem.
, vol.26
, pp. 1752-1780
-
-
Banks, J.L.1
Beard, H.S.2
Cao, Y.X.3
Cho, A.E.4
Damm, W.5
Farid, R.6
Felts, A.K.7
Halgren, T.A.8
Mainz, D.T.9
Maple, J.R.10
Murphy, R.11
Philipp, D.M.12
Repasky, M.P.13
Zhang, L.Y.14
Berne, B.J.15
Friesner, R.A.16
Gallicchio, E.17
Levy, R.M.18
-
41
-
-
84986437005
-
-
10.1002/jcc.540110405
-
F. Mohamadi, N. G. J. Richards, W. C. Guida, R. Liskamp, M. Lipton, C. Caufield, G. Chang, T. Hendrickson, and W. C. Still, J. Comput. Chem. 11, 440-467 (1990). 10.1002/jcc.540110405
-
(1990)
J. Comput. Chem.
, vol.11
, pp. 440-467
-
-
Mohamadi, F.1
Richards, N.G.J.2
Guida, W.C.3
Liskamp, R.4
Lipton, M.5
Caufield, C.6
Chang, G.7
Hendrickson, T.8
Still, W.C.9
-
42
-
-
3042524904
-
-
10.1021/j100142a004
-
C. I. Bayly, P. Cieplak, W. D. Cornell, and P. A. Kollman, J. Phys. Chem. 97, 10269-10280 (1993). 10.1021/j100142a004
-
(1993)
J. Phys. Chem.
, vol.97
, pp. 10269-10280
-
-
Bayly, C.I.1
Cieplak, P.2
Cornell, W.D.3
Kollman, P.A.4
-
43
-
-
84879096487
-
-
GAUSSIAN 09, Revision A.01, Gaussian, Inc., Wallingford, CT
-
M. J. Frisch, G. Trucks, H. Schlegel, GAUSSIAN 09, Revision A.01, Gaussian, Inc., Wallingford, CT, 2009.
-
(2009)
-
-
Frisch, M.J.1
Trucks, G.2
Schlegel, H.3
-
44
-
-
33748538349
-
-
10.1016/j.mgm.2005.12.005
-
J. Wang, W. Wang, P. A. Kollman, and D. A. Case, J. Mol. Graphics Modell. 25 (2), 247-260 (2006). 10.1016/j.mgm.2005.12.005
-
(2006)
J. Mol. Graphics Modell.
, vol.25
, Issue.2
, pp. 247-260
-
-
Wang, J.1
Wang, W.2
Kollman, P.A.3
Case, D.A.4
-
45
-
-
77954566051
-
-
10.1039/c0cp00111b
-
F. Y. Dupradeau, A. Pigache, T. Zaffran, C. Savineau, R. Lelong, N. Grivel, D. Lelong, W. Rosanski, and P. Cieplak, Phys. Chem. Chem. Phys. 12, 7821-7839 (2010). 10.1039/c0cp00111b
-
(2010)
Phys. Chem. Chem. Phys.
, vol.12
, pp. 7821-7839
-
-
Dupradeau, F.Y.1
Pigache, A.2
Zaffran, T.3
Savineau, C.4
Lelong, R.5
Grivel, N.6
Lelong, D.7
Rosanski, W.8
Cieplak, P.9
-
47
-
-
0004016501
-
-
10.1063/1.445869
-
W. L. Jorgensen, J. Chandrasekhar, J. D. Madura, R. W. Impey, and M. L. Klein, J. Chem. Phys. 79, 926-935 (1983). 10.1063/1.445869
-
(1983)
J. Chem. Phys.
, vol.79
, pp. 926-935
-
-
Jorgensen, W.L.1
Chandrasekhar, J.2
Madura, J.D.3
Impey, R.W.4
Klein, M.L.5
-
48
-
-
46249092554
-
-
10.1021/ct700301q
-
B. Hess, C. Kutzner, D. van der Spoel, and E. Lindahl, J. Chem. Theory Comput. 4, 435-447 (2008). 10.1021/ct700301q
-
(2008)
J. Chem. Theory Comput.
, vol.4
, pp. 435-447
-
-
Hess, B.1
Kutzner, C.2
Van Der Spoel, D.3
Lindahl, E.4
-
50
-
-
5244304444
-
-
10.1016/0021-9991(76)90078-4
-
C. H. Bennett, J. Comput. Phys. 22, 245-268 (1976). 10.1016/0021-9991(76) 90078-4
-
(1976)
J. Comput. Phys.
, vol.22
, pp. 245-268
-
-
Bennett, C.H.1
-
52
-
-
33750587438
-
-
10.1063/1.448118
-
H. J. C. Berendsen, J. P. M. Postma, W. F. Vangunsteren, A. Dinola, and J. R. Haak, J. Chem. Phys. 81, 3684-3690 (1984). 10.1063/1.448118
-
(1984)
J. Chem. Phys.
, vol.81
, pp. 3684-3690
-
-
Berendsen, H.J.C.1
Postma, J.P.M.2
Vangunsteren, W.F.3
Dinola, A.4
Haak, J.R.5
-
53
-
-
33645961739
-
-
10.1063/1.470117
-
U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee, and L. G. Pedersen, J. Chem. Phys. 103, 8577-8593 (1995). 10.1063/1.470117
-
(1995)
J. Chem. Phys.
, vol.103
, pp. 8577-8593
-
-
Essmann, U.1
Perera, L.2
Berkowitz, M.L.3
Darden, T.4
Lee, H.5
Pedersen, L.G.6
-
56
-
-
0000682989
-
-
10.1002/(SICI)1096-987X(19970130)18:2<268::AID-JCC11>3.0.CO;2-E
-
R. E. Bruccoleri, J. Novotny, and M. E. Davis, J. Comput. Chem. 18, 268-276 (1997). 10.1002/(SICI)1096-987X(19970130)18:2<268::AID-JCC11>3.0. CO;2-E
-
(1997)
J. Comput. Chem.
, vol.18
, pp. 268-276
-
-
Bruccoleri, R.E.1
Novotny, J.2
Davis, M.E.3
-
57
-
-
0017429069
-
-
10.1146/annurev.bb.06.060177.001055
-
F. M. Richards, Annu. Rev. Biophys. Bioeng. 6, 151-176 (1977). 10.1146/annurev.bb.06.060177.001055
-
(1977)
Annu. Rev. Biophys. Bioeng.
, vol.6
, pp. 151-176
-
-
Richards, F.M.1
-
58
-
-
84865138151
-
-
10.1021/jp305226j
-
A. Mukhopadhyay, A. T. Fenley, I. S. Tolokh, and A. V. Onufriev, J. Phys. Chem. B 116, 9776-9783 (2012). 10.1021/jp305226j
-
(2012)
J. Phys. Chem. B
, vol.116
, pp. 9776-9783
-
-
Mukhopadhyay, A.1
Fenley, A.T.2
Tolokh, I.S.3
Onufriev, A.V.4
-
62
-
-
84866521607
-
-
10.1021/ja303309e
-
F. Biedermann, V. D. Uzunova, O. A. Scherman, W. M. Nau, and A. De Simone, J. Am. Chem. Soc. 134, 15318-15323 (2012). 10.1021/ja303309e
-
(2012)
J. Am. Chem. Soc.
, vol.134
, pp. 15318-15323
-
-
Biedermann, F.1
Uzunova, V.D.2
Scherman, O.A.3
Nau, W.M.4
De Simone, A.5
-
63
-
-
84872145772
-
-
10.1021/ct300515n
-
K. E. Rogers, J. M. Ortiz-Sanchez, R. Baron, M. Fajer, C. A. F. de Oliveira, and J. A. McCammon, J. Chem. Theory Comput. 9 (1), 46-53, (2013). 10.1021/ct300515n
-
(2013)
J. Chem. Theory Comput.
, vol.9
, Issue.1
, pp. 46-53
-
-
Rogers, K.E.1
Ortiz-Sanchez, J.M.2
Baron, R.3
Fajer, M.4
De Oliveira, C.A.F.5
McCammon, J.A.6
-
64
-
-
0141990949
-
-
10.1063/1.1587119
-
M. R. Shirts, J. W. Pitera, W. C. Swope, and V. S. Pande, J. Chem. Phys. 119, 5740-5761 (2003). 10.1063/1.1587119
-
(2003)
J. Chem. Phys.
, vol.119
, pp. 5740-5761
-
-
Shirts, M.R.1
Pitera, J.W.2
Swope, W.C.3
Pande, V.S.4
-
66
-
-
67650084578
-
-
10.1021/jp809782z
-
C. J. Fennell, A. Bizjak, V. Vlachy, and K. A. Dill, J. Phys. Chem. B 113, 6782-6791 (2009). 10.1021/jp809782z
-
(2009)
J. Phys. Chem. B
, vol.113
, pp. 6782-6791
-
-
Fennell, C.J.1
Bizjak, A.2
Vlachy, V.3
Dill, K.A.4
-
68
-
-
33748496457
-
-
10.1021/j100385a008
-
H. E. Alper and R. M. Levy, J. Phys. Chem. 94, 8401-8403 (1990). 10.1021/j100385a008
-
(1990)
J. Phys. Chem.
, vol.94
, pp. 8401-8403
-
-
Alper, H.E.1
Levy, R.M.2
-
70
-
-
49349094023
-
-
10.1021/jp711339d
-
S. Gavryushov, J. Phys. Chem. B 112, 8955-8965 (2008). 10.1021/jp711339d
-
(2008)
J. Phys. Chem. B
, vol.112
, pp. 8955-8965
-
-
Gavryushov, S.1
-
71
-
-
79954517621
-
-
10.1021/cr100130d
-
Y. Marcus, Chem. Rev. 111, 2761-2783 (2011). 10.1021/cr100130d
-
(2011)
Chem. Rev.
, vol.111
, pp. 2761-2783
-
-
Marcus, Y.1
-
72
-
-
51149203218
-
-
10.1063/1.1733864
-
E. Whalley, J. Chem. Phys. 38, 1400 (1963). 10.1063/1.1733864
-
(1963)
J. Chem. Phys.
, vol.38
, pp. 1400
-
-
Whalley, E.1
-
74
-
-
58749107160
-
-
10.1529/biophysj.108.131649
-
C. Azuara, H. Orland, M. Bon, P. Koehl, and M. Delarue, Biophys. J. 95, 5587-5605 (2008). 10.1529/biophysj.108.131649
-
(2008)
Biophys. J.
, vol.95
, pp. 5587-5605
-
-
Azuara, C.1
Orland, H.2
Bon, M.3
Koehl, P.4
Delarue, M.5
-
76
-
-
40549111312
-
-
10.1021/jp709958f
-
D. L. Mobley, A. E. Barber, C. J. Fennell, and K. A. Dill, J. Phys. Chem. B 112, 2405-2414 (2008). 10.1021/jp709958f
-
(2008)
J. Phys. Chem. B
, vol.112
, pp. 2405-2414
-
-
Mobley, D.L.1
Barber, A.E.2
Fennell, C.J.3
Dill, K.A.4
-
77
-
-
33749637456
-
-
10.1021/j100347a081
-
B. Jayaram, R. Fine, K. Sharp, and B. Honig, J. Phys. Chem. 93, 4320-4327 (1989). 10.1021/j100347a081
-
(1989)
J. Phys. Chem.
, vol.93
, pp. 4320-4327
-
-
Jayaram, B.1
Fine, R.2
Sharp, K.3
Honig, B.4
-
78
-
-
0001025176
-
-
10.1063/1.476650
-
J. K. Hyun and T. Ichiye, J. Chem. Phys. 109, 1074-1083 (1998). 10.1063/1.476650
-
(1998)
J. Chem. Phys.
, vol.109
, pp. 1074-1083
-
-
Hyun, J.K.1
Ichiye, T.2
-
79
-
-
84865454330
-
-
10.1063/1.4742910
-
S. A. Hassan, J. Chem. Phys. 137, 074102 (2012). 10.1063/1.4742910
-
(2012)
J. Chem. Phys.
, vol.137
, pp. 074102
-
-
Hassan, S.A.1
-
84
-
-
84879088374
-
-
See supplementary material at http://dx.doi.org/10.1063/1.4808376 E-JCPSA6-138-054322 for Tables S1 and S2 and Figures S1-S3.
-
-
-
|