-
1
-
-
0346726109
-
-
(a) Garcia-Viloca, M.; Gao, J.; Karplus, M.; Truhlar, D. G. Science 2004, 303, 186.
-
(2004)
Science
, vol.303
, pp. 186
-
-
Garcia-Viloca, M.1
Gao, J.2
Karplus, M.3
Truhlar, D.G.4
-
4
-
-
33846512402
-
-
Rueda, M.; Ferrer, C.; Meyer, T.; Pérez, A.; Camps, J.; Hospital, A.; Gelṕ, J. L.; Orozco, M. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 796.
-
(d) Rueda, M.; Ferrer, C.; Meyer, T.; Pérez, A.; Camps, J.; Hospital, A.; Gelṕ, J. L.; Orozco, M. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 796.
-
-
-
-
10
-
-
36649029525
-
-
Xie, W.; Pu, J.; MacKerell, A. D., Jr.; Gao, J. J. Chem. Theory Comput. 2007, 3, 1878. For a thematic issue devoted to current research on polarization and polarizable force fields, see:
-
(a) Xie, W.; Pu, J.; MacKerell, A. D., Jr.; Gao, J. J. Chem. Theory Comput. 2007, 3, 1878. For a thematic issue devoted to current research on polarization and polarizable force fields, see:
-
-
-
-
16
-
-
0035039453
-
-
For a historical account of the development of the Lifsonstyle force field, see
-
For a historical account of the development of the Lifsonstyle force field, see Levitt, M. Nat. Struct. Mol. Biol. 2001, 8, 392.
-
(2001)
Nat. Struct. Mol. Biol
, vol.8
, pp. 392
-
-
Levitt, M.1
-
17
-
-
0017776823
-
-
McCammon, J. A.; Gelin, B. R.; Karplus, M. Nature 1977, 267, 585.
-
(1977)
Nature
, vol.267
, pp. 585
-
-
McCammon, J.A.1
Gelin, B.R.2
Karplus, M.3
-
18
-
-
0029912748
-
-
Jorgensen, W. L.; Maxwell, D. S.; Tirado-Rives, J. J. Am. Chem. Soc. 1996, 118, 11225.
-
(1996)
J. Am. Chem. Soc
, vol.118
, pp. 11225
-
-
Jorgensen, W.L.1
Maxwell, D.S.2
Tirado-Rives, J.3
-
19
-
-
0041784950
-
-
MacKerell, A. D., Jr.; Bashford, D.; Bellott, M.; Dunbrack, R. L.; Evanseck, J. D.; Field, M. J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F. T. K.; Mattos, C.; Michnick, S.; Ngo, T.; Nguyen, D. T.; Prodhom, B.; Reiher, W. E., III.; Roux, B.; Schlenkrich, M.; Smith, J. C.; Stote, R.; Straub, J.; Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M. J. Phys. Chem. B 1998, 102, 3586.
-
MacKerell, A. D., Jr.; Bashford, D.; Bellott, M.; Dunbrack, R. L.; Evanseck, J. D.; Field, M. J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F. T. K.; Mattos, C.; Michnick, S.; Ngo, T.; Nguyen, D. T.; Prodhom, B.; Reiher, W. E., III.; Roux, B.; Schlenkrich, M.; Smith, J. C.; Stote, R.; Straub, J.; Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M. J. Phys. Chem. B 1998, 102, 3586.
-
-
-
-
20
-
-
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
-
21
-
-
21244467488
-
-
Oostenbrink, C.; Soares, T. A.; van der Vegt, N. F. A.; van Gunsteren, W. F. Eur. Biophys. J. 2005, 34, 273.
-
(2005)
Eur. Biophys. J
, vol.34
, pp. 273
-
-
Oostenbrink, C.1
Soares, T.A.2
van der Vegt, N.F.A.3
van Gunsteren, W.F.4
-
22
-
-
0004479272
-
-
Maple, J. R.; Hwang, M. J.; Jalkanen, K. J.; Stockfisch, T. P.; Hagler, A. T. J. Comput. Chem. 1998, 19, 430.
-
(1998)
J. Comput. Chem
, vol.19
, pp. 430
-
-
Maple, J.R.1
Hwang, M.J.2
Jalkanen, K.J.3
Stockfisch, T.P.4
Hagler, A.T.5
-
24
-
-
0023598484
-
-
Van Belle, D.; Couplet, I.; Prevost, M.; Wodak, S. J. J. Mol. Biol. 1987, 198, 721.
-
(1987)
J. Mol. Biol
, vol.198
, pp. 721
-
-
Van Belle, D.1
Couplet, I.2
Prevost, M.3
Wodak, S.J.4
-
25
-
-
33751553825
-
-
Niesar, U.; Corongiu, G.; Clementi, E.; Kneller, G. R.; Bhattacharya, D. K. J. Phys. Chem. 1990, 94, 7949.
-
(1990)
J. Phys. Chem
, vol.94
, pp. 7949
-
-
Niesar, U.1
Corongiu, G.2
Clementi, E.3
Kneller, G.R.4
Bhattacharya, D.K.5
-
26
-
-
2042467135
-
-
Sprik, M.; Klein, M. L.; Watanabe, K. J. Phys. Chem. 1990, 94, 6483.
-
(1990)
J. Phys. Chem
, vol.94
, pp. 6483
-
-
Sprik, M.1
Klein, M.L.2
Watanabe, K.3
-
28
-
-
36448999850
-
-
(a) Rick, S.; Stuart, S.; Berne, B. J. Chem. Phys. 1994, 101, 6141.
-
(1994)
J. Chem. Phys
, vol.101
, pp. 6141
-
-
Rick, S.1
Stuart, S.2
Berne, B.3
-
29
-
-
0036882094
-
-
(b) Kaminski, G. A.; Stern, H. A.; Berne, B. J.; Friesner, R. A.; Cao, Y. X.; Murphy, R. B.; Zhou, R.; Halgren, T. A. J. Comput. Chem. 2002, 23, 1515.
-
(2002)
J. Comput. Chem
, vol.23
, pp. 1515
-
-
Kaminski, G.A.1
Stern, H.A.2
Berne, B.J.3
Friesner, R.A.4
Cao, Y.X.5
Murphy, R.B.6
Zhou, R.7
Halgren, T.A.8
-
30
-
-
30444431852
-
-
(c) Maple, J. R.; Cao, Y.; Damm, W.; Halgren, T. A.; Kaminski, G. A.; Zhang, L. Y.; Friesner, R. A. J. Chem. Theory. Comput. 2005, 1, 694.
-
(2005)
J. Chem. Theory. Comput
, vol.1
, pp. 694
-
-
Maple, J.R.1
Cao, Y.2
Damm, W.3
Halgren, T.A.4
Kaminski, G.A.5
Zhang, L.Y.6
Friesner, R.A.7
-
31
-
-
0000140870
-
-
Ding, Y.; Bernardo, D. N.; Krogh-Jespersen, K.; Levy, R. M. J. Phys. Chem. 1995, 99, 11575.
-
(1995)
J. Phys. Chem
, vol.99
, pp. 11575
-
-
Ding, Y.1
Bernardo, D.N.2
Krogh-Jespersen, K.3
Levy, R.M.4
-
32
-
-
33751156912
-
-
(a) Gao, J.; Habibollazadeh, D.; Shao, L. J. Phys. Chem. 1995, 99, 16460.
-
(1995)
J. Phys. Chem
, vol.99
, pp. 16460
-
-
Gao, J.1
Habibollazadeh, D.2
Shao, L.3
-
33
-
-
0001379843
-
-
(b) Gao, J.; Pavelites, J. J.; Habibollazadeh, D. J. Phys. Chem. 1996, 100, 2689.
-
(1996)
J. Phys. Chem
, vol.100
, pp. 2689
-
-
Gao, J.1
Pavelites, J.J.2
Habibollazadeh, D.3
-
34
-
-
0035974484
-
-
Cieplak, P.; Caldwell, J.; Kollman, P. J. Comput. Chem. 2001, 22, 1048.
-
(2001)
J. Comput. Chem
, vol.22
, pp. 1048
-
-
Cieplak, P.1
Caldwell, J.2
Kollman, P.3
-
36
-
-
0346850017
-
-
(b) Grossfield, A.; Ren, P.; Ponder, J. W. J. Am. Chem. Soc. 2003, 125, 15671.
-
(2003)
J. Am. Chem. Soc
, vol.125
, pp. 15671
-
-
Grossfield, A.1
Ren, P.2
Ponder, J.W.3
-
37
-
-
33947591301
-
-
(c) Rasmussen, T. D.; Ren, P.; Ponder, J. W.; Jensen, F. Int. J. Quantum Chem. 2007, 107, 1390.
-
(2007)
Int. J. Quantum Chem
, vol.107
, pp. 1390
-
-
Rasmussen, T.D.1
Ren, P.2
Ponder, J.W.3
Jensen, F.4
-
39
-
-
0037456452
-
-
Cubero, E.; Luque, F. J.; Orozco, M.; Gao, J. J. Phys. Chem. B 2003, 107, 1664.
-
(2003)
J. Phys. Chem. B
, vol.107
, pp. 1664
-
-
Cubero, E.1
Luque, F.J.2
Orozco, M.3
Gao, J.4
-
41
-
-
7444226283
-
-
(b) Ogawa, T.; Kuita, N.; Sekino, H.; Kitao, O.; Tanaka, S. Chem. Phys. Lett. 2004, 397, 382.
-
(2004)
Chem. Phys. Lett
, vol.397
, pp. 382
-
-
Ogawa, T.1
Kuita, N.2
Sekino, H.3
Kitao, O.4
Tanaka, S.5
-
44
-
-
36649019360
-
-
Soteras, I.; Curutchet, C.; Bidon-Chanal, A.; Dehez, F.; Angyan, J. G.; Orozco, M.; Chipot, C.; Luque, J. J. Chem. Theory Comput. 2007, 3, 1901.
-
(2007)
J. Chem. Theory Comput
, vol.3
, pp. 1901
-
-
Soteras, I.1
Curutchet, C.2
Bidon-Chanal, A.3
Dehez, F.4
Angyan, J.G.5
Orozco, M.6
Chipot, C.7
Luque, J.8
-
47
-
-
0142242177
-
-
Wierzchowski, S. J.; Kofke, D. A.; Gao, J. J. Chem. Phys. 2003, 119, 7365.
-
(2003)
J. Chem. Phys
, vol.119
, pp. 7365
-
-
Wierzchowski, S.J.1
Kofke, D.A.2
Gao, J.3
-
49
-
-
47249085107
-
-
Xie, W.; Song, L.; Truhlar, D.; Gao, J. J. Chem. Phys. 2008, 128, 234108.
-
(2008)
J. Chem. Phys
, vol.128
, pp. 234108
-
-
Xie, W.1
Song, L.2
Truhlar, D.3
Gao, J.4
-
50
-
-
57049120521
-
-
Xie, W.; Song, L.; Truhlar, D.; Gao, J. J. Phys. Chem. B 2008, 112, 14124.
-
(2008)
J. Phys. Chem. B
, vol.112
, pp. 14124
-
-
Xie, W.1
Song, L.2
Truhlar, D.3
Gao, J.4
-
52
-
-
65249175212
-
-
Pure Appl. Chem. 1974 40 291 See also: Moss, G. P. Abbre Viations and Symbols for the Description of the Conformation of Polypeptide Chains, IUPAC-IUB Commission on Biochemical Nomenclature (CBN): London, 1974. Available at http://www.chem.qmul.ac.uk/iupac/misc/ppep1.html (accessed Dec 20, 2008).
-
Pure Appl. Chem. 1974 40 291 See also: Moss, G. P. Abbre Viations and Symbols for the Description of the Conformation of Polypeptide Chains, IUPAC-IUB Commission on Biochemical Nomenclature (CBN): London, 1974. Available at http://www.chem.qmul.ac.uk/iupac/misc/ppep1.html (accessed Dec 20, 2008).
-
-
-
-
53
-
-
0000411659
-
-
(a) Gao, J.; Amara, P.; Alhambra, C.; Field, M. J. J. Phys. Chem. A 1998, 102, 4714.
-
(1998)
J. Phys. Chem. A
, vol.102
, pp. 4714
-
-
Gao, J.1
Amara, P.2
Alhambra, C.3
Field, M.J.4
-
54
-
-
0034375393
-
-
(b) Amara, P.; Field, M. J.; Alhambra, C.; Gao, J. Theor. Chem. Acc. 2000, 104, 336.
-
(2000)
Theor. Chem. Acc
, vol.104
, pp. 336
-
-
Amara, P.1
Field, M.J.2
Alhambra, C.3
Gao, J.4
-
56
-
-
84986513644
-
-
Field, M. J.; Bash, P. A.; Karplus, M. J. Comput. Chem. 1990, 11, 700.
-
(1990)
J. Comput. Chem
, vol.11
, pp. 700
-
-
Field, M.J.1
Bash, P.A.2
Karplus, M.3
-
60
-
-
0842341771
-
-
Dewar, M. J. S.; Zoebisch, E. G.; Healy, E. F.; Stewart, J. J. P. J. Am. Chem. Soc. 1985, 107, 3902.
-
(1985)
J. Am. Chem. Soc
, vol.107
, pp. 3902
-
-
Dewar, M.J.S.1
Zoebisch, E.G.2
Healy, E.F.3
Stewart, J.J.P.4
-
62
-
-
84986512474
-
-
Brooks, B. R.; Bruccoleri, R. E.; Olafson, B. D.; States, D. J.; Swaminathan, S.; Karplus, M. J. Comput. Chem. 1983, 4, 187.
-
(1983)
J. Comput. Chem
, vol.4
, pp. 187
-
-
Brooks, B.R.1
Bruccoleri, R.E.2
Olafson, B.D.3
States, D.J.4
Swaminathan, S.5
Karplus, M.6
-
63
-
-
0004016501
-
-
Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. J. Chem. Phys. 1983, 79, 926.
-
(1983)
J. Chem. Phys
, vol.79
, pp. 926
-
-
Jorgensen, W.L.1
Chandrasekhar, J.2
Madura, J.D.3
Impey, R.W.4
Klein, M.L.5
-
66
-
-
33646940952
-
-
Ryckaert, J. P.; Ciccotti, G.; Berendsen, H. J. C. J. Comput. Phys. 1977, 23, 327.
-
(1977)
J. Comput. Phys
, vol.23
, pp. 327
-
-
Ryckaert, J.P.1
Ciccotti, G.2
Berendsen, H.J.C.3
-
67
-
-
42149100111
-
-
Walker, R. C.; Crowley, M. F.; Case, D. A. J. Comput. Chem. 2008, 29, 1019.
-
(2008)
J. Comput. Chem
, vol.29
, pp. 1019
-
-
Walker, R.C.1
Crowley, M.F.2
Case, D.A.3
-
69
-
-
84962459967
-
-
(b) Gao, J.; Luque, F. J.; Orozco, M. J. Chem. Phys. 1993, 98, 2975.
-
(1993)
J. Chem. Phys
, vol.98
, pp. 2975
-
-
Gao, J.1
Luque, F.J.2
Orozco, M.3
-
70
-
-
0029248338
-
-
(a) Storer, J. W.; Giesen, D. J.; Cramer, C. J.; Truhlar, D. G. J. Comput.-Aided Mol. Des. 1995, 9, 87.
-
(1995)
J. Comput.-Aided Mol. Des
, vol.9
, pp. 87
-
-
Storer, J.W.1
Giesen, D.J.2
Cramer, C.J.3
Truhlar, D.G.4
-
71
-
-
33748905333
-
-
(b) Chambers, C. C.; Cramer, C. J.; Truhlar, D. G. J. Phys. Chem. 1996, 100, 16385.
-
(1996)
J. Phys. Chem
, vol.100
, pp. 16385
-
-
Chambers, C.C.1
Cramer, C.J.2
Truhlar, D.G.3
-
72
-
-
0000958036
-
-
(c) Li, J.; Zhu, T.; Cramer, C. J.; Truhlar, D. G. J. Phys. Chem. A 1998, 102, 1820.
-
(1998)
J. Phys. Chem. A
, vol.102
, pp. 1820
-
-
Li, J.1
Zhu, T.2
Cramer, C.J.3
Truhlar, D.G.4
-
73
-
-
84962345519
-
-
(d) Kelly, C. P.; Cramer, C. J.; Truhlar, D. G. J. Chem. Theory Comput. 2005, 1, 1133.
-
(2005)
J. Chem. Theory Comput
, vol.1
, pp. 1133
-
-
Kelly, C.P.1
Cramer, C.J.2
Truhlar, D.G.3
-
75
-
-
15244349932
-
-
Chipot, C.; Á ngyán, J. G. New J. Chem. 2005, 29, 411.
-
(b) Chipot, C.; Á ngyán, J. G. New J. Chem. 2005, 29, 411.
-
-
-
-
76
-
-
33947392043
-
-
(a) Heyden, A.; Lin, H.; Truhlar, D. G. J. Phys. Chem. B 2007, 111, 2231.
-
(2007)
J. Phys. Chem. B
, vol.111
, pp. 2231
-
-
Heyden, A.1
Lin, H.2
Truhlar, D.G.3
-
78
-
-
0344391945
-
-
Garcia-Viloca, M.; Truhar, D. G.; Gao, J. Biochemistry 2003, 42, 13558.
-
(2003)
Biochemistry
, vol.42
, pp. 13558
-
-
Garcia-Viloca, M.1
Truhar, D.G.2
Gao, J.3
-
79
-
-
1542305706
-
-
Spiegel, K.; Rothlisberger, U.; Carloni, P. J. Phys. Chem. B 2004, 108, 2699.
-
(2004)
J. Phys. Chem. B
, vol.108
, pp. 2699
-
-
Spiegel, K.1
Rothlisberger, U.2
Carloni, P.3
-
80
-
-
36248999961
-
-
Rodriguez, A.; Oliva, C.; Gonzalez, M.; Van der Kamp, M.; Mulholland, A. J. J. Phys. Chem. B 2007, 111, 12909.
-
(2007)
J. Phys. Chem. B
, vol.111
, pp. 12909
-
-
Rodriguez, A.1
Oliva, C.2
Gonzalez, M.3
Van der Kamp, M.4
Mulholland, A.J.5
-
83
-
-
0003010379
-
-
Keyes, D. E, Saad, Y, Truhlar, D. G, Eds, SIAM: Philadelphia
-
(b) Stechel, E. B. In Domain-Based Parallelism and Problem Decomposition Methods in Computational Science and Engineering; Keyes, D. E., Saad, Y., Truhlar, D. G., Eds.; SIAM: Philadelphia, 1995; pp 217-238.
-
(1995)
Domain-Based Parallelism and Problem Decomposition Methods in Computational Science and Engineering
, pp. 217-238
-
-
Stechel, E.B.1
-
84
-
-
0031141966
-
-
(c) Bowler, D. R.; Aoki, M.; Goringe, C. M.; Horsfield, A. P.; Pettifor, D. G. Modell. Simul. Mater. Sci. Eng. 1997, 5, 199.
-
(1997)
Modell. Simul. Mater. Sci. Eng
, vol.5
, pp. 199
-
-
Bowler, D.R.1
Aoki, M.2
Goringe, C.M.3
Horsfield, A.P.4
Pettifor, D.G.5
-
86
-
-
0034301415
-
-
(e) Gogonea, V.; Westerhoff, L. M.; Merz, K. M., Jr. J. Chem. Phys. 2000, 113, 5604.
-
(2000)
J. Chem. Phys
, vol.113
, pp. 5604
-
-
Gogonea, V.1
Westerhoff, L.M.2
Merz Jr., K.M.3
-
87
-
-
17044393550
-
-
(f) Shimojo, F.; Kalia, R. K.; Nakano, A.; Vashishta, P. Comput. Phys. Commun. 2005, 167, 151.
-
(2005)
Comput. Phys. Commun
, vol.167
, pp. 151
-
-
Shimojo, F.1
Kalia, R.K.2
Nakano, A.3
Vashishta, P.4
|