-
1
-
-
0027267249
-
-
Goodman, M. F.; Creighton, S.; Bloom, L. B.; Petruska, J. Crit. Rev. Biochem. Mol. Biol. 1993, 28, 83.
-
(1993)
Crit. Rev. Biochem. Mol. Biol.
, vol.28
, pp. 83
-
-
Goodman, M.F.1
Creighton, S.2
Bloom, L.B.3
Petruska, J.4
-
2
-
-
0023154067
-
-
Sowers, L. C.; Shaw, B. R.; Veigl, M. L.; Sedwick, W. D. Mutat. Res. 1987, 177, 201.
-
(1987)
Mutat. Res.
, vol.177
, pp. 201
-
-
Sowers, L.C.1
Shaw, B.R.2
Veigl, M.L.3
Sedwick, W.D.4
-
3
-
-
0023049968
-
-
Sowers, L. C.; Fazakerley, G. V.; Kim, H.; Dalton, L.; Goodman, M. F. Biochemistry 1986, 25, 3983.
-
(1986)
Biochemistry
, vol.25
, pp. 3983
-
-
Sowers, L.C.1
Fazakerley, G.V.2
Kim, H.3
Dalton, L.4
Goodman, M.F.5
-
4
-
-
0026582206
-
-
Boulard, Y.; Cognet, J. A. H.; Gabarro-Arpa, J.; Le Bret, M.; Sowers, L. C.; Fazakerley, G. V. Nucleic Acids Res. 1992, 20, 1933.
-
(1992)
Nucleic Acids Res.
, vol.20
, pp. 1933
-
-
Boulard, Y.1
Cognet, J.A.H.2
Gabarro-Arpa, J.3
Le Bret, M.4
Sowers, L.C.5
Fazakerley, G.V.6
-
5
-
-
0023664782
-
-
Hunter, W. N.; Brown, T.; Kennard, O. Nucleic Acids Res. 1987, 15, 6589.
-
(1987)
Nucleic Acids Res.
, vol.15
, pp. 6589
-
-
Hunter, W.N.1
Brown, T.2
Kennard, O.3
-
6
-
-
0025346833
-
-
Brown, T.; Leonard, G. A.; Booth, E. D.; Kneale, G. J. Mol. Biol. 1990, 212, 437.
-
(1990)
J. Mol. Biol.
, vol.212
, pp. 437
-
-
Brown, T.1
Leonard, G.A.2
Booth, E.D.3
Kneale, G.4
-
8
-
-
0027297046
-
-
Yu, H.; Eritja, R.; Bloom, L. B.; Goodman, M. F. J. Biol. Chem. 1993, 268, 15935.
-
(1993)
J. Biol. Chem.
, vol.268
, pp. 15935
-
-
Yu, H.1
Eritja, R.2
Bloom, L.B.3
Goodman, M.F.4
-
9
-
-
0023790393
-
-
Sowers, L. C.; Eritja, R.; Kaplan, B.; Goodman, M. F.; Fazakerly, G. V. J. Biol. Chem. 1988, 263, 14794.
-
(1988)
J. Biol. Chem.
, vol.263
, pp. 14794
-
-
Sowers, L.C.1
Eritja, R.2
Kaplan, B.3
Goodman, M.F.4
Fazakerly, G.V.5
-
12
-
-
0030967829
-
-
Moran, S.; Ren, R. X. F.; Kool, E. T. Proc. Natl. Acad. Sci. U.S.A. 1997, 94, 10506.
-
(1997)
Proc. Natl. Acad. Sci. U.S.A.
, vol.94
, pp. 10506
-
-
Moran, S.1
Ren, R.X.F.2
Kool, E.T.3
-
13
-
-
0029011701
-
-
Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K. M., Jr.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman, P. A. J. Am. Chem. Soc. 1995, 117, 5179.
-
(1995)
J. Am. Chem. Soc.
, vol.117
, pp. 5179
-
-
Cornell, W.D.1
Cieplak, P.2
Bayly, C.I.3
Gould, I.R.4
Merz Jr., K.M.5
Ferguson, D.M.6
Spellmeyer, D.C.7
Fox, T.8
Caldwell, J.W.9
Kollman, P.A.10
-
14
-
-
0032232405
-
-
Marelius, J.; Kolmodin, K.; Feierberg, I.; Åqvist, J. J. Mol. Graphics Model. 1999, 16, 213.
-
(1999)
J. Mol. Graphics Model.
, vol.16
, pp. 213
-
-
Marelius, J.1
Kolmodin, K.2
Feierberg, I.3
Åqvist, J.4
-
15
-
-
0029170114
-
-
Cheatham T. E., III; Miller, J. L.; Fox, T.; Darden, T. A.; Kollman, P. A. J. Am. Chem. Soc. 1995, 117, 4193.
-
(1995)
J. Am. Chem. Soc.
, vol.117
, pp. 4193
-
-
Cheatham III, T.E.1
Miller, J.L.2
Fox, T.3
Darden, T.A.4
Kollman, P.A.5
-
17
-
-
0033595533
-
-
Cubero, E.; Sherer, E. C.; Luque, F. J.; Orozco, M.; Laughton, C. A. J. Am. Chem. Soc. 1999, 121, 8653.
-
(1999)
J. Am. Chem. Soc.
, vol.121
, pp. 8653
-
-
Cubero, E.1
Sherer, E.C.2
Luque, F.J.3
Orozco, M.4
Laughton, C.A.5
-
18
-
-
0032556243
-
-
Jayaram, B.; Sprous, D.; Young, M. A.; Beveridge, D. L. J. Am. Chem. Soc. 1998, 120, 10629.
-
(1998)
J. Am. Chem. Soc.
, vol.120
, pp. 10629
-
-
Jayaram, B.1
Sprous, D.2
Young, M.A.3
Beveridge, D.L.4
-
19
-
-
0031782289
-
-
Pardo, L.; Pastor, N.; Weinstein, H. Biophys. J. 1998, 75, 2411.
-
(1998)
Biophys. J.
, vol.75
, pp. 2411
-
-
Pardo, L.1
Pastor, N.2
Weinstein, H.3
-
20
-
-
0031749572
-
-
Spackova, N.; Berger, I.; Egli, M.; Sponer, J. J. Am. Chem. Soc. 1998, 120, 6147.
-
(1998)
J. Am. Chem. Soc.
, vol.120
, pp. 6147
-
-
Spackova, N.1
Berger, I.2
Egli, M.3
Sponer, J.4
-
21
-
-
0002467371
-
-
van Gunsteren, W. F., Wiener, P. K., Eds.; ESCOM: Leiden
-
Warshel, A.; Creighton, S. In Computer simulation of biomolecular Systems; van Gunsteren, W. F., Wiener, P. K., Eds.; ESCOM: Leiden, 1989; pp 120.
-
(1989)
Computer Simulation of Biomolecular Systems
, pp. 120
-
-
Warshel, A.1
Creighton, S.2
-
22
-
-
0027536101
-
-
Goodsell, D. S.; Kopka, M. L.; Cascio, D.; Dickerson, R. E. Proc. Natl. Acad. Sci. U.S.A. 1993, 90, 2930.
-
(1993)
Proc. Natl. Acad. Sci. U.S.A.
, vol.90
, pp. 2930
-
-
Goodsell, D.S.1
Kopka, M.L.2
Cascio, D.3
Dickerson, R.E.4
-
23
-
-
84983715113
-
-
Tripos Inc., 1699 South Hanley Rd., St. Louis, Missouri, 63144
-
SYBYL 6.6; Tripos Inc., 1699 South Hanley Rd., St. Louis, Missouri, 63144.
-
SYBYL 6.6
-
-
-
24
-
-
0033585580
-
-
Tereshko, V.; Minasov, G.; Egli, M. J. Am. Chem. Soc. 1999, 121, 470.
-
(1999)
J. Am. Chem. Soc.
, vol.121
, pp. 470
-
-
Tereshko, V.1
Minasov, G.2
Egli, M.3
-
29
-
-
0032342086
-
-
Lipkowitz, K. B., Boyd, D. B.,Eds.; Wiley-VCH: New York
-
Meirovitch, H. In Reviews in Computational Chemistry; Lipkowitz, K. B., Boyd, D. B.,Eds.; Wiley-VCH: New York, 1998; Vol. 12; pp 1.
-
(1998)
Reviews in Computational Chemistry
, vol.12
, pp. 1
-
-
Meirovitch, H.1
-
31
-
-
0032541103
-
-
Shih, P.; Pedersen, L. G.; Gibbs, P. R.; Wolfenden, R. J. Mol. Biol. 1998, 280, 421.
-
(1998)
J. Mol. Biol.
, vol.280
, pp. 421
-
-
Shih, P.1
Pedersen, L.G.2
Gibbs, P.R.3
Wolfenden, R.4
-
33
-
-
84962349365
-
-
Florián, J.; Sponer, J.; Warshel, A. J. Phys. Chem. B 1999, 103, 884.
-
(1999)
J. Phys. Chem. B
, vol.103
, pp. 884
-
-
Florián, J.1
Sponer, J.2
Warshel, A.3
-
34
-
-
9944232242
-
-
Cabani, S.; Gianni, P.; Mollica, V.; Lepori, L. J. Solution Chem. 1981, 10, 563.
-
(1981)
J. Solution Chem.
, vol.10
, pp. 563
-
-
Cabani, S.1
Gianni, P.2
Mollica, V.3
Lepori, L.4
-
35
-
-
0029758746
-
-
Law, S. M.; Eritja, R.; Goodman, M. F.; Breslauer, K. J. Biochemistry 1996, 35, 12329.
-
(1996)
Biochemistry
, vol.35
, pp. 12329
-
-
Law, S.M.1
Eritja, R.2
Goodman, M.F.3
Breslauer, K.J.4
-
36
-
-
33645930898
-
-
note
-
One should realize, however, that a complete exploration of the available configuration space or a "complete" convergence is an unrealistic goal for any current simulation method because of computer time limitations. A realistic goal is to obtain sufficient convergence in the quantity under consideration without running infinitely long trajectories. This is why we have developped the SCAAS and LRF methods, which attempt to obtain reasonable convergence in electrostatic energies. As with any related scientific problem it is essential to examine whether one could reproduce the relevant observed quantity, while realizing that no simulation is perfect. In doing so, it is much more important to examine sensitivity to different boundary conditions and long-range treatments than to run one very long trajectory.
-
-
-
-
37
-
-
0029188718
-
-
Alden, R. G.; Parson, W. W.; Chu, Z. T.; Warshel, A. J. Am. Chem. Soc. 1995, 117, 12284.
-
(1995)
J. Am. Chem. Soc.
, vol.117
, pp. 12284
-
-
Alden, R.G.1
Parson, W.W.2
Chu, Z.T.3
Warshel, A.4
-
38
-
-
0000728542
-
-
Lee, F. S., Chu, Z. T., Warshel, A. J. Comput. Chem. 1993, 14, 161.
-
(1993)
J. Comput. Chem.
, vol.14
, pp. 161
-
-
Lee, F.S.1
Chu, Z.T.2
Warshel, A.3
-
40
-
-
0000671518
-
-
Sham, Y. Y.; Chu, Z. T.; Warshel, A. J. Phys. Chem. B 1997, 101, 4458.
-
(1997)
J. Phys. Chem. B
, vol.101
, pp. 4458
-
-
Sham, Y.Y.1
Chu, Z.T.2
Warshel, A.3
-
41
-
-
0033609515
-
-
Fuxreiter, M.; Warshel, A.; Osman, R. Biochemistry 1999, 38, 9577.
-
(1999)
Biochemistry
, vol.38
, pp. 9577
-
-
Fuxreiter, M.1
Warshel, A.2
Osman, R.3
-
42
-
-
0031790169
-
-
Guckian, K. M.; Krugh, T. R.; Kool, E. T. Nature Struct. Biol. 1998, 5, 954.
-
(1998)
Nature Struct. Biol.
, vol.5
, pp. 954
-
-
Guckian, K.M.1
Krugh, T.R.2
Kool, E.T.3
-
43
-
-
0022423486
-
-
Aboul-ela, F.; Koh, D.; Tinoco, I., Jr.; Martin, F. H. Nucleic Acids Res. 1985, 13, 4811.
-
(1985)
Nucleic Acids Res.
, vol.13
, pp. 4811
-
-
Aboul-ela, F.1
Koh, D.2
Tinoco Jr., I.3
Martin, F.H.4
-
44
-
-
0022263018
-
-
Brown, T.; Kennard, O.; Kneale, G.; Rabinovich, D. Nature 1985, 315, 604.
-
(1985)
Nature
, vol.315
, pp. 604
-
-
Brown, T.1
Kennard, O.2
Kneale, G.3
Rabinovich, D.4
-
45
-
-
0023664744
-
-
Hunter, W. N.; Brown, T.; Kneale, G.; Anand, N. N.; Rabinovich, D.; Kennard, O. J. Biol. Chem. 1987, 262, 9962.
-
(1987)
J. Biol. Chem.
, vol.262
, pp. 9962
-
-
Hunter, W.N.1
Brown, T.2
Kneale, G.3
Anand, N.N.4
Rabinovich, D.5
Kennard, O.6
-
47
-
-
0029968822
-
-
SantaLucia J., Jr.; Allawi, H. T.; Senevirante, P. A. Biochemistry 1996, 35, 3555.
-
(1996)
Biochemistry
, vol.35
, pp. 3555
-
-
Santalucia Jr., J.1
Allawi, H.T.2
Senevirante, P.A.3
-
48
-
-
0000141714
-
-
Wang, C.; Gao, H.; Gaffney, B. L.; Jones, R. A. J. Am. Chem. Soc. 1991, 113, 5486.
-
(1991)
J. Am. Chem. Soc.
, vol.113
, pp. 5486
-
-
Wang, C.1
Gao, H.2
Gaffney, B.L.3
Jones, R.A.4
-
49
-
-
85088174716
-
-
note
-
25 (TG/AC step) = -0.26-0.14 + 1.12 + 1.72 = 2.4 ± 0.4 kcal/mol. The error range was estimated by assuming 0.1 kcal/mol uncertainty for each nearest neighbor parameter.
-
-
-
-
50
-
-
0028049441
-
-
Pelletier, H.; Sawaya, M. R.; Kumar, A.; Wilson, S. H.; Kraut, J. Science 1994, 264, 1891.
-
(1994)
Science
, vol.264
, pp. 1891
-
-
Pelletier, H.1
Sawaya, M.R.2
Kumar, A.3
Wilson, S.H.4
Kraut, J.5
-
51
-
-
0000124775
-
-
Petruska, J.; Goodman, M. F.; Boosalis, M. S.; Sowers, L. C. Proc. Natl. Acad. Sci. U.S.A. 1988, 85, 6252.
-
(1988)
Proc. Natl. Acad. Sci. U.S.A.
, vol.85
, pp. 6252
-
-
Petruska, J.1
Goodman, M.F.2
Boosalis, M.S.3
Sowers, L.C.4
-
55
-
-
84902459099
-
-
in press
-
Villà, J.; Strajbl, M.; Glennon, T. M.; Sham, Y. Y.; Chu, Z.-T.; Warshel, A. Proc. Natl. Acad. Sci. U.S.A., in press.
-
Proc. Natl. Acad. Sci. U.S.A.
-
-
Villà, J.1
Strajbl, M.2
Glennon, T.M.3
Sham, Y.Y.4
Chu, Z.-T.5
Warshel, A.6
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