-
2
-
-
0028170376
-
-
Wilson, K. P.; Black, J. A. F.; Thomson, J. A.; Kim, E. E.; Griffith, J. P.; Navia, M. A.; Murcko, M. A.; Chambers, S. P.; Aldape, R. A.; Raybuck S. A.; Livingston, D. J. Nature 1994, 370, 270.
-
(1994)
Nature
, vol.370
, pp. 270
-
-
Wilson, K.P.1
Black, J.A.F.2
Thomson, J.A.3
Kim, E.E.4
Griffith, J.P.5
Navia, M.A.6
Murcko, M.A.7
Chambers, S.P.8
Aldape, R.A.9
Raybuck, S.A.10
Livingston, D.J.11
-
6
-
-
0026003243
-
-
Menard, R.; Carriere, J.; Laflamme, P.; Plouffe, C.; Khouri, H. E.; Vernet, T.; Tessier, D. C.; Thomas, D. Y.; Storer, A. C. Biochemistry 1991, 30, 8924.
-
(1991)
Biochemistry
, vol.30
, pp. 8924
-
-
Menard, R.1
Carriere, J.2
Laflamme, P.3
Plouffe, C.4
Khouri, H.E.5
Vernet, T.6
Tessier, D.C.7
Thomas, D.Y.8
Storer, A.C.9
-
7
-
-
0027418741
-
-
Mellor, G. W.; Sreedharan, S. K.; Kowlessur, D.; Thomas, E. W.; Brocklehurst, K. Biochem. J. 1993, 290, 75.
-
(1993)
Biochem. J.
, vol.290
, pp. 75
-
-
Mellor, G.W.1
Sreedharan, S.K.2
Kowlessur, D.3
Thomas, E.W.4
Brocklehurst, K.5
-
8
-
-
0029590248
-
-
Dufour, E.; Storer, A. C.; Menard, R. Biochemistry 1995, 34, 16 382.
-
(1995)
Biochemistry
, vol.34
, pp. 16382
-
-
Dufour, E.1
Storer, A.C.2
Menard, R.3
-
9
-
-
14444269890
-
-
Webber, S. E.; Okano, K.; Little, T. L.; Reich, S. H.; Xin, Y.; Fuhrman, S. A.; Matthews, D. A.; Love, R. A.; Hendrickson, T. F.; Patick, A. K.; Meador, J. W.; Ferre, R. A.; Brown, E. L.; Ford, C. E.; Binford, S. L.; Worland, S. T. J. Med. Chem. 1998, 41, 2786.
-
(1998)
J. Med. Chem.
, vol.41
, pp. 2786
-
-
Webber, S.E.1
Okano, K.2
Little, T.L.3
Reich, S.H.4
Xin, Y.5
Fuhrman, S.A.6
Matthews, D.A.7
Love, R.A.8
Hendrickson, T.F.9
Patick, A.K.10
Meador, J.W.11
Ferre, R.A.12
Brown, E.L.13
Ford, C.E.14
Binford, S.L.15
Worland, S.T.16
-
13
-
-
0000420069
-
-
Keillor, J. W.; Neverov, A. A.; Brown, R. S. J. Am. Chem. Soc. 1994, 116, 4669.
-
(1994)
J. Am. Chem. Soc.
, vol.116
, pp. 4669
-
-
Keillor, J.W.1
Neverov, A.A.2
Brown, R.S.3
-
16
-
-
84962335857
-
-
Ehrenberg, R., Graslund, A., Nilsson, L., Ed.: Springer-Verlag: New York
-
Warshel, A., In Structure, Dynamics and Functions of Biomolecules; Ehrenberg, R., Graslund, A., Nilsson, L., Ed.: Springer-Verlag: New York, 1987; p 60.
-
(1987)
Structure, Dynamics and Functions of Biomolecules
, pp. 60
-
-
Warshel, A.1
-
17
-
-
0024538543
-
-
Warshel, A.; Naray-Szabo, G.; Sussman, F.; Hwang, J.-K. Biochemistry 1989, 28, 3629.
-
(1989)
Biochemistry
, vol.28
, pp. 3629
-
-
Warshel, A.1
Naray-Szabo, G.2
Sussman, F.3
Hwang, J.-K.4
-
21
-
-
11644294259
-
-
Bentzien, J.; MUller, R. P.; Florian, J.; Warshel, A. J. Phys. Chem. B 1998, 102, 2293.
-
(1998)
J. Phys. Chem. B
, vol.102
, pp. 2293
-
-
Bentzien, J.1
Muller, R.P.2
Florian, J.3
Warshel, A.4
-
22
-
-
0033567033
-
-
Kolmodin, K.; Nordlund, P.; Aqvist, J. Proteins 1999, 36, 370.
-
(1999)
Proteins
, vol.36
, pp. 370
-
-
Kolmodin, K.1
Nordlund, P.2
Aqvist, J.3
-
26
-
-
0025276611
-
-
Arad, D.; Langridge, R.: Kollman, P. A. J. Am. Chem. Soc. 1990, 112, 491.
-
(1990)
J. Am. Chem. Soc.
, vol.112
, pp. 491
-
-
Arad, D.1
Langridge, R.2
Kollman, P.A.3
-
27
-
-
0001683589
-
-
Duncan, G.D.; Huber, C. P.; Welsh, W. J. J. Am. Chem. Soc. 1992, 114, 5784.
-
(1992)
J. Am. Chem. Soc.
, vol.114
, pp. 5784
-
-
Duncan, G.D.1
Huber, C.P.2
Welsh, W.J.3
-
29
-
-
0003028115
-
-
Harrison, M. J.; Burton, N. A.; Hillier, I. H.; Gould, I. R. Chem. Commun. 1996, 2769.
-
(1996)
Chem. Commun.
, vol.2769
-
-
Harrison, M.J.1
Burton, N.A.2
Hillier, I.H.3
Gould, I.R.4
-
30
-
-
0031576658
-
-
Harrison, M. J.; Burton, N. A.; Hillier, I. H. J. Am. Chem. Soc. 1997, 119, 12285.
-
(1997)
J. Am. Chem. Soc.
, vol.119
, pp. 12285
-
-
Harrison, M.J.1
Burton, N.A.2
Hillier, I.H.3
-
31
-
-
0032897320
-
-
Han, W.-G.; Tajkhorshid, E.; Suhai, S. J. Biomol. Struct. Dyn. 1999, 16, 1019.
-
(1999)
J. Biomol. Struct. Dyn.
, vol.16
, pp. 1019
-
-
Han, W.-G.1
Tajkhorshid, E.2
Suhai, S.3
-
33
-
-
0041561440
-
-
University of Southern California: Los Angeles
-
Florián, J.; Warshel, A. ChemSol; University of Southern California: Los Angeles, 1998.
-
(1998)
ChemSol
-
-
Florián, J.1
Warshel, A.2
-
34
-
-
84946893847
-
-
Miertus, S.; Scrocco, E.; Tomasi, J. Chem. Phys. 1981, 55, 117.
-
(1981)
Chem. Phys.
, vol.55
, pp. 117
-
-
Miertus, S.1
Scrocco, E.2
Tomasi, J.3
-
37
-
-
0034616816
-
-
Strajbl, M.; Florián, J.; Warshel, A. J. Am. Chem. Soc. 2000, 122, 5354.
-
(2000)
J. Am. Chem. Soc.
, vol.122
, pp. 5354
-
-
Strajbl, M.1
Florián, J.2
Warshel, A.3
-
38
-
-
0032508930
-
-
Florián, J.; Åqvist, J.; Warshel, A. J. Am. Chem. Soc. 1998, 120, 11524
-
(1998)
J. Am. Chem. Soc.
, vol.120
, pp. 11524
-
-
Florián, J.1
Åqvist, J.2
Warshel, A.3
-
39
-
-
0003109106
-
-
Strajbl, M.; Florián, J.; Warshel, A. Int. J. Quantum. Chem. 2000, 77, 44.
-
(2000)
Int. J. Quantum. Chem.
, vol.77
, pp. 44
-
-
Strajbl, M.1
Florián, J.2
Warshel, A.3
-
46
-
-
0034710867
-
-
Villa, J.; Strajbl, M.; Glennon, T. M.; Sham, Y. Y.; Chu, Z. T.; Warshel, A. Proc. Natl. Acad. Sci. U.S.A. 97, 11 899.
-
(2000)
Proc. Natl. Acad. Sci. U.S.A.
, vol.97
, pp. 11899
-
-
Villa, J.1
Strajbl, M.2
Glennon, T.M.3
Sham, Y.Y.4
Chu, Z.T.5
Warshel, A.6
-
47
-
-
0000997465
-
-
Strajbl, M.; Sham, Y. Y.; Villa, J.; Chu, Z. T.; Warshel, A. J. Phys. Chem. 2000, 104, 4578.
-
(2000)
J. Phys. Chem.
, vol.104
, pp. 4578
-
-
Strajbl, M.1
Sham, Y.Y.2
Villa, J.3
Chu, Z.T.4
Warshel, A.5
-
52
-
-
0001414996
-
-
Kong, J.; White, C. A.; Krylov, A. I.; Sherrill, D.; Adamson, R. D.; Furlani, T. R.; Lee, M. S.; Lee, A. M.; Gwaltney, S. R.; Adams, T. R.; Ochsenself, C.; Gilbert, A. T. B.; Kedziora, G. S.; Rassolov, V. A.; Maurice, D. R.; Nair, N.; Shao, Y.; Besley, N. A.; Maslen, P. E.; Dombroski, J. P.; Daschel, H.; Zhang, W.; Korambath, P. P.; Baker, J.; Byrd, E. F. C.; Voorhis, T. V.; Oumi, M.; Hirata, S.; Hsu, C.-P.; Ishikawa, N.; Florián, J.; Warshel, A.; Johnson, B. G.; Gill, P. M. W.; Head-Gordon, M.; Pople, J. A. J. Comput. Chem. 2000, 21, 1532.
-
(2000)
J. Comput. Chem.
, vol.21
, pp. 1532
-
-
Kong, J.1
White, C.A.2
Krylov, A.I.3
Sherrill, D.4
Adamson, R.D.5
Furlani, T.R.6
Lee, M.S.7
Lee, A.M.8
Gwaltney, S.R.9
Adams, T.R.10
Ochsenself, C.11
Gilbert, A.T.B.12
Kedziora, G.S.13
Rassolov, V.A.14
Maurice, D.R.15
Nair, N.16
Shao, Y.17
Besley, N.A.18
Maslen, P.E.19
Dombroski, J.P.20
Daschel, H.21
Zhang, W.22
Korambath, P.P.23
Baker, J.24
Byrd, E.F.C.25
Voorhis, T.V.26
Oumi, M.27
Hirata, S.28
Hsu, C.-P.29
Ishikawa, N.30
Florián, J.31
Warshel, A.32
Johnson, B.G.33
Gill, P.M.W.34
Head-Gordon, M.35
Pople, J.A.36
more..
-
53
-
-
0010922186
-
-
Gaussian, Inc.: Pittsburgh
-
Gaussian94 (Revision D.2); Gaussian, Inc.: Pittsburgh, 1995.
-
(1995)
Gaussian94 (Revision D.2)
-
-
-
54
-
-
84962335991
-
-
note
-
relax) and with our PCM/LD model and found no significant differences between these two models. Thus, we believe that our results for the ion-pair region of the reaction surface are sufficiently reliable.
-
-
-
-
55
-
-
0345913518
-
-
Gao, J., Thompson, M. A., Eds.; American Chemical Society: Washington, DC
-
Bentzien, J.; Florián, J.; Glennon, T.; Warshel, A. in Combined Quantum Mechanical & Molecular Mechanical Methods; Gao, J., Thompson, M. A., Eds.; American Chemical Society: Washington, DC, 1998; Vol. 712; pp 16.
-
(1998)
Combined Quantum Mechanical & Molecular Mechanical Methods
, vol.712
, pp. 16
-
-
Bentzien, J.1
Florián, J.2
Glennon, T.3
Warshel, A.4
-
56
-
-
0041401966
-
-
Curtiss, L. A.; Raghavachari, K.; Trucks, G. W.; Pople, J. A. J. Chem.
-
(1991)
J. Chem. Phys.
, vol.94
, pp. 7221
-
-
Curtiss, L.A.1
Raghavachari, K.2
Trucks, G.W.3
Pople, J.A.4
-
57
-
-
36449002507
-
-
Curtiss, L. A.; Raghavachari, K.; Pople, J. A. J. Chem. Phys. 1993, 98, 1293.
-
(1993)
J. Chem. Phys.
, vol.98
, pp. 1293
-
-
Curtiss, L.A.1
Raghavachari, K.2
Pople, J.A.3
-
69
-
-
0041600218
-
-
Wang, J.-K.; King, G.; Creighton, S.; Warshel, A. J. Am. Chem. Soc. 1988, 110, 5297.
-
(1988)
J. Am. Chem. Soc.
, vol.110
, pp. 5297
-
-
Wang, J.-K.1
King, G.2
Creighton, S.3
Warshel, A.4
-
77
-
-
84962335982
-
-
note
-
The calculated G2/solvation free energies were -627.684 830 au/-8.1 kcal/mol, and -627.133 110 au/-76.8 kcal/mol for the neutral and anionic TI, respectively.
-
-
-
-
78
-
-
33845379042
-
-
Chandrasekhar, J.; Smith, S. F.; Jorgensen, W. L. J. Am. Chem. Soc. 1985, 107, 154.
-
(1985)
J. Am. Chem. Soc.
, vol.107
, pp. 154
-
-
Chandrasekhar, J.1
Smith, S.F.2
Jorgensen, W.L.3
-
80
-
-
0035155864
-
-
Kollman, P. A.; Kuhn, B.; Donini, O.; Perakyla, M.; Stanton, R.; Bakowies, D. Acc. Chem. Res. 2001, 34, 72.
-
(2001)
Acc. Chem. Res.
, vol.34
, pp. 72
-
-
Kollman, P.A.1
Kuhn, B.2
Donini, O.3
Perakyla, M.4
Stanton, R.5
Bakowies, D.6
-
82
-
-
0030917908
-
-
Amzel, L. M. Proteins: Structure, Function, and Genetics 1997, 28, 144.
-
(1997)
Proteins: Structure, Function, and Genetics
, vol.28
, pp. 144
-
-
Amzel, L.M.1
-
86
-
-
84962353067
-
-
note
-
solv term. Also note that the 11.7 kcal/mol includes 3.9 kcal/mol solvation contribution.
-
-
-
-
87
-
-
2642622572
-
-
Stanton, R. V.; Peräkylä, M.; Bakowies, D.; Kollman, P. J. Am. Chem. Soc. 1998, 120, 3448.
-
(1998)
J. Am. Chem. Soc.
, vol.120
, pp. 3448
-
-
Stanton, R.V.1
Peräkylä, M.2
Bakowies, D.3
Kollman, P.4
-
90
-
-
84962456734
-
-
note
-
Because a referee of this paper criticized footnote 61 in our previous paper, we would like to here explain hwy we think that the activation entropy of 11.4 kcal/mol reported by Stanton et al. was not obtained by proper calculations. That is, the suggestion that Hermans' approach was used in the entropy calculations of Stanton et al. is problematic. Hermans' approach is a restrain release approach (RRA), whereas Stanton et al. merely assumed arbitrarily the configurational volume in the enzyme and then they used the corresponding force contants in a formula provided by Hermans to obtain the entropy. The point is that the assumed configurational volume directly determines the entropy s the use of Hermanns' formula was unnecessary and does not constitute a RRA calculation.
-
-
-
-
92
-
-
84962405119
-
-
note
-
w
-
-
-
-
94
-
-
0000855438
-
-
Mihel, I.; Knipe, J. O.; Coward, J. K.; Schowen, R. L. J. Am. Chem. Soc. 1979, 101, 4349.
-
(1979)
J. Am. Chem. Soc.
, vol.101
, pp. 4349
-
-
Mihel, I.1
Knipe, J.O.2
Coward, J.K.3
Schowen, R.L.4
-
95
-
-
0026000470
-
-
Khouri, H. E.; Vernet, T.; Menard, R.; Parlati, F.; Laflamme, P.; Tessier, D. C.; Gour-Salin, B.; Thomas, D. Y.; Storer, A. C. Biochemistry 1991, 30, 8929.
-
(1991)
Biochemistry
, vol.30
, pp. 8929
-
-
Khouri, H.E.1
Vernet, T.2
Menard, R.3
Parlati, F.4
Laflamme, P.5
Tessier, D.C.6
Gour-Salin, B.7
Thomas, D.8
Storer, A.C.9
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