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Journal of Chemical Physics
Volumn 117, Issue 9, 2002, Pages 4184-4200
Constant-pH molecular dynamics using stochastic titration
(3)
Baptista, António M
a
Teixeira, Vitor H
a
Soares, Cláudio M
a
a
INSTITUTO DE TECNOLOGIA QUÍMICA E BIOLÓGICA
(
Portugal
)
Author keywords
[No Author keywords available]
Indexed keywords
ALGORITHMS; BINDING ENERGY; COMPUTER SIMULATION; CONTINUUM MECHANICS; DISSOCIATION; ELECTROSTATICS; ENTROPY; FREE ENERGY; HAMILTONIANS; ISOMERIZATION; MONTE CARLO METHODS; PARAMETER ESTIMATION; PH EFFECTS; PROTEINS; PROTONS; TITRATION;
PROTONATION;
MOLECULAR DYNAMICS;
EID
:
0036732086
PISSN
:
00219606
EISSN
:
None
Source Type
:
Journal
DOI
:
10.1063/1.1497164
Document Type
:
Article
Times cited : (
286
)
References (
131
)
1
0018094892
(1978)
Science
, vol.201
, pp. 1187
Perutz, M.F.
1
2
0000357781
(1979)
J. Phys. Chem.
, vol.83
, pp. 1640
Warshel, A.
1
3
0021476470
(1984)
Q. Rev. Biophys.
, vol.17
, pp. 283
Warshel, A.
1
Russell, S.T.
2
4
0021935830
(1985)
Annu. Rev. Biophys. Biophys. Chem.
, vol.14
, pp. 387
Matthew, J.B.
1
5
0022485888
(1986)
Annu. Rev. Biophys. Biophys. chem.
, vol.15
, pp. 163
Honig, B.H.
1
6
0025283002
(1990)
Annu. Rev. Biophys. Biophys. Chem.
, vol.19
, pp. 301
Sharp, K.A.
1
Honig, B.
2
7
0025891413
(1991)
Annu. Rev. Biophys. Biophys. Chem.
, vol.20
, pp. 267
Warshel, A.
1
Aqvist, J.
2
8
0000240916
(1996)
Biotechnol. Annu. Rev.
, vol.2
, pp. 315
Martel, P.J.
1
Baptista, A.
2
Petersen, S.B.
3
9
0032233055
(1998)
Annu. Rev. Phys. Chem.
, vol.49
, pp. 531
Levy, R.M.
1
Gallicchio, E.
2
10
0033024177
(1999)
Annu. Rev. Biophys. Biomol. Struct.
, vol.28
, pp. 155
Sagui, C.
1
Darden, T.A.
2
11
0034039797
(2000)
Curr. Opin. Struct. Biol.
, vol.10
, pp. 153
Sheinerman, F.B.
1
Norel, R.
2
Honig, B.
3
12
0003932768
Freeman, New York
(1984)
Proteins, 1st ed.
Creighton, T.E.
1
13
0003481596
Freeman, New York
(1985)
Enzyme Structure and Mechanism, 2nd ed.
Fersht, A.R.
1
14
0002511411
(1924)
C R. Trav. Lab. Carlsberg
, vol.15
, pp. 1
Linderstrøm-Lang, K.
1
15
33947468892
(1957)
J. Am. Chem. Soc.
, vol.79
, pp. 5333
Tanford, C.
1
Kirkwood, J.G.
2
16
0017100947
(1976)
J. Mol. Biol.
, vol.103
, pp. 227
Warshel, A.
1
Levitt, M.
2
17
0017608499
(1977)
Ann. N.Y. Acad. Sci.
, vol.303
, pp. 22
Orttung, W.H.
1
18
0019889036
(1981)
Biochemistry
, vol.20
, pp. 3167
Warshel, A.
1
19
0020475509
(1982)
J. Mol. Biol.
, vol.157
, pp. 671
Warwicker, J.
1
Watson, H.C.
2
20
0022429751
(1985)
J. Mol. Biol.
, vol.186
, pp. 815
Zauhar, R.J.
1
Morgan, R.S.
2
21
0023060081
(1986)
Biochemistry
, vol.25
, pp. 8368
Warshel, A.
1
Sussman, F.
2
King, G.
3
22
0025197061
(1990)
Biochemistry
, vol.29
, pp. 10219
Bashford, D.
1
Karplus, M.
2
23
0026012015
(1991)
Biophys. J.
, vol.59
, pp. 670
Simonson, T.
1
Perahia, D.
2
Brünger, A.
3
24
0028169692
(1994)
Proteins: Struct., Funct., Genet.
, vol.20
, pp. 85
Del Buono, G.S.
1
Figueirido, F.E.
2
Levy, R.M.
3
25
0026612756
(1992)
J. Mol. Biol.
, vol.224
, pp. 473
Bashford, D.
1
Gerwert, K.
2
26
0027219184
(1993)
Biochemistry
, vol.32
, pp. 8045
Bashford, D.
1
Case, D.A.
2
Dalvit, C.
3
Tennant, L.
4
Wright, P.E.
5
27
0027563464
(1993)
Proteins: Struct., Funct., Genet.
, vol.15
, pp. 252
Yang, A.-S.
1
Gunner, M.R.
2
Sampogna, R.
3
Sharp, K.
4
Honig, B.
5
28
0027231258
(1993)
J. Mol. Biol.
, vol.231
, pp. 459
Yang, A.-S.
1
Honig, B.
2
29
0027209697
(1993)
Biophys. J.
, vol.65
, pp. 48
Oberoi, H.
1
Allewell, N.M.
2
30
0000728542
(1993)
J. Comput. Chem.
, vol.14
, pp. 161
Lee, F.S.
1
Chu, Z.T.
2
Warshel, A.
3
31
0028305457
(1994)
J. Mol. Biol.
, vol.238
, pp. 415
Antosiewicz, J.
1
McCammon, J.A.
2
Gilson, M.K.
3
32
0028859420
(1995)
Biophys. J.
, vol.69
, pp. 1721
You, T.J.
1
Bashford, D.
2
33
0029665693
(1996)
Biochemistry
, vol.35
, pp. 7819
Antosiewicz, J.
1
McCammon, J.A.
2
Gilson, M.K.
3
34
33748400070
(1996)
J. Phys. Chem.
, vol.100
, pp. 20156
Beroza, P.
1
Case, D.A.
2
35
33748593093
(1996)
J. Phys. Chem.
, vol.100
, pp. 17373
Demchuk, E.
1
Wade, R.C.
2
36
0029976726
(1996)
Biophys. J.
, vol.71
, pp. 138
Gibas, C.J.
1
Subramanian, S.
2
37
0030945495
(1997)
Biophys. J.
, vol.72
, pp. 2075
Alexov, E.G.
1
Gunner, M.R.
2
38
0000671518
(1997)
J. Phys. Chem.
, vol.101
, pp. 4458
Sham, Y.Y.
1
Chu, Z.T.
2
Warshel, A.
3
39
0031564641
(1997)
J. Mol. Biol.
, vol.267
, pp. 1002
Zhou, H.-X.
1
Vijayakumar, M.
2
40
0035120969
(2001)
J. Phys. Chem. B
, vol.105
, pp. 293
Baptista, A.M.
1
Soares, C.M.
2
41
0031076776
(1997)
J. Phys. Chem. B
, vol.101
, pp. 1663
Schaefer, M.
1
Sommer, M.
2
Karplus, M.
3
42
0030030176
(1996)
Biophys. J.
, vol.70
, pp. 2469
Lancaster, C.R.D.
1
Michel, H.
2
Honig, B.
3
Gunner, M.R.
4
43
0031458937
(1997)
J. Biol. Inorg. Chem.
, vol.2
, pp. 714
Soares, C.M.
1
Martel, P.J.
2
Carrondo, M.A.
3
44
0031880698
(1998)
Biophys. J.
, vol.74
, pp. 708
Kannt, A.
1
Lancaster, C.R.D.
2
Michel, H.
3
45
0032588946
(1999)
J. Biol. Inorg. Chem.
, vol.4
, pp. 73
Martel, P.J.
1
46
0033001692
(1999)
Biophys. J.
, vol.76
, pp. 2978
Bapfista, A.M.
1
Martel, P.J.
2
Soares, C.M.
3
47
0036359052
(2002)
J. Biol. Inorg. Chem.
, vol.7
, pp. 200
Teixeira, V.H.
1
Soares, C.M.
2
Baptista, A.M.
3
48
0035941269
(2001)
J. Biol. Chem.
, vol.276
, pp. 44044
Louro, R.O.
1
49
33845183931
(1989)
J. Am. Chem. Soc.
, vol.111
, pp. 4190
Jorgensen, W.L.
1
Briggs, J.M.
2
50
0000053068
(1994)
J. Am. Chem. Soc.
, vol.116
, pp. 8238
Rajasekaran, E.
1
Jayaram, B.
2
Honig, B.
3
51
0000431645
(1994)
J. Am. Chem. Soc.
, vol.116
, pp. 10298
Potter, M.J.
1
Gilson, M.K.
2
McCammon, J.A.
3
52
33751159055
(1994)
J. Phys. Chem.
, vol.98
, pp. 11059
Chen, J.L.
1
Noodleman, L.
2
Bashford, D.
3
53
0001625211
(1996)
J. Phys. Chem.
, vol.100
, pp. 6389
Figueirido, F.
1
Del Buono, G.S.
2
Levy, R.M.
3
54
0031358013
(1997)
J. Phys. Chem. A
, vol.101
, pp. 10075
Topol, I.A.
1
Tawa, G.J.
2
Burt, S.K.
3
Rashin, A.A.
4
55
0031779284
(1998)
J. Am. Chem. Soc.
, vol.120
, pp. 6138
Luo, R.
1
Head, M.S.
2
Moult, J.
3
Gilson, M.K.
4
56
0035827113
(2001)
J. Chem. Phys.
, vol.114
, pp. 9706
Börjesson, U.
1
Hünenberger, P.
2
57
84961978266
(2001)
J. Chem. Phys.
, vol.114
, pp. 4595
Toth, A.M.
1
Liptak, M.D.
2
Phillips, D.L.
3
Shields, G.C.
4
58
0000135791
(1995)
J. Phys. Chem.
, vol.103
, pp. 150
Tuckerman, M.E.
1
Laasonen, K.
2
Sprik, M.
3
Parrinello, M.
4
59
0000420846
(2000)
Chem. Phys. Lett.
, vol.321
, pp. 225
Geissler, P.L.
1
Dellago, C.
2
Chandler, D.
3
Hutter, J.
4
Parrinello, M.
5
60
4243810035
(1993)
Chem. Rev.
, vol.93
, pp. 2523
Aqvist, J.
1
Warshel, A.
2
61
33748659289
(1996)
J. Phys. Chem.
, vol.100
, pp. 2535
Bała, P.
1
Grochowski, P.
2
Lesyng, B.
3
McCammon, J.A.
4
62
0033751528
(2000)
J. Phys. Chem. A
, vol.104
, pp. 3276
Billeter, S.R.
1
Van Gunsteren, W.F.
2
63
0034274389
(2000)
J. Phys. Chem. A
, vol.104
, pp. 8283
Lill, M.A.
1
Hutter, M.C.
2
Helms, V.
3
64
5544264558
(1991)
J. Chem. Phys.
, vol.95
, pp. 3627
Levy, R.M.
1
Belhadj, M.
2
Kitchen, D.B.
3
65
0026611315
(1992)
J. Mol. Biol.
, vol.224
, pp. 589
Langen, R.
1
66
0028093487
(1994)
Biophys. Chem.
, vol.51
, pp. 167
Rashin, A.A.
1
Bukatin, M.A.
2
67
0029016182
(1995)
Science
, vol.268
, pp. 1144
Honig, B.
1
Nicholls, A.
2
68
0024788820
(1989)
Biochemistry
, vol.28
, pp. 10072
Antosiewicz, J.
1
Porschke, D.
2
69
0026095641
(1991)
Proc. Natl. Acad. Sci. U.S.A.
, vol.88
, pp. 5804
Beroza, P.
1
Fredkin, D.R.
2
Okamura, M.Y.
3
Feher, G.
4
70
0001247046
(1991)
J. Phys. Chem.
, vol.95
, pp. 9956
Bashford, D.
1
Karplus, M.
2
71
0027477251
(1993)
Proteins: Struct., Funct., Genet.
, vol.15
, pp. 266
Gilson, M.K.
1
72
0000174762
(1999)
J. Comput. Chem.
, vol.20
, pp. 1091
Spassov, V.
1
Bashford, D.
2
73
0010624785
(1998)
Biophys. J.
, vol.74
, pp. 1744
Sham, Y.Y.
1
Muegge, I.
2
Warshel, A.
3
74
0000083584
(1991)
J. Chem. Phys.
, vol.95
, pp. 4366
King, G.
1
Lee, F.S.
2
Warshel, A.
3
75
0028876827
(1995)
Proc. Natl. Acad. Sci. U.S.A.
, vol.92
, pp. 1082
Simonson, T.
1
Perahia, D.
2
76
0029833446
(1996)
J. Am. Chem. Soc.
, vol.118
, pp. 8452
Simonson, T.
1
Brooks C.L. III
2
77
0024519351
(1989)
Proteins: Struct., Funct., Genet.
, vol.5
, pp. 78
Harvey, S.C.
1
78
0032054517
(1998)
Curr. Opin. Struct. Biol.
, vol.8
, pp. 211
Warshel, A.
1
Papazyan, A.
2
79
0000875502
(1999)
J. Phys. Chem. B
, vol.103
, pp. 6142
Simonson, T.
1
Archontis, G.
2
Karplus, M.
3
80
0036140263
(2002)
Proteins: Struct., Funct., Genet.
, vol.46
, pp. 41
Gorfe, A.A.
1
81
0031052519
(1997)
Protein Sci.
, vol.6
, pp. 373
Wlodek, S.T.
1
Antosiewicz, J.
2
McCammon, J.A.
3
82
0031670370
(1998)
Proteins: Struct., Funct., Genet.
, vol.33
, pp. 145
Van Vlijmen, H.W.T.
1
Schaefer, M.
2
Karplus, M.
3
83
0035960203
(2001)
J. Phys. Chem. B
, vol.105
, pp. 9339
Koumanov, A.
1
Karshikoff, A.
2
Friis, E.P.
3
Borchert, T.V.
4
84
0031719963
(1998)
Eur. Biophys. J.
, vol.27
, pp. 626
Rabenstein, B.
1
Ullmann, G.M.
2
Knapp, E.-W.
3
85
0030582736
(1996)
J. Mol. Biol.
, vol.264
, pp. 770
Ripoll, D.R.
1
Vorobjev, Y.N.
2
Liwo, A.
3
Vila, J.A.
4
Scheraga, H.A.
5
86
0033578683
(1999)
J. Mol. Biol.
, vol.292
, pp. 431
Ripoll, D.R.
1
Vila, J.A.
2
Villegas, M.E.
3
Scheraga, H.A.
4
87
0024566409
(1989)
Biochemistry
, vol.28
, pp. 3188
Cutler, R.L.
1
88
0030828226
(1997)
J. Phys. Chem. B
, vol.101
, pp. 825
Muegge, I.
1
Qi, P.X.
2
Wand, A.J.
3
Chu, Z.T.
4
Warshel, A.
5
89
0033614791
(1999)
Biochemistry
, vol.38
, pp. 8253
Alexov, E.G.
1
Gunner, M.R.
2
90
0030970305
(1997)
Proteins: Struct., Funct., Genet.
, vol.27
, pp. 523
Baptista, A.M.
1
Martel, P.J.
2
Petersen, S.B.
3
91
0036573188
(2002)
J. Chem. Phys.
, vol.116
, pp. 7766
Baptista, A.M.
1
92
0002899271
(1991)
Mol. Simul.
, vol.6
, pp. 5
Çaǧin, T.
1
Pettitt, B.M.
2
93
7044233785
(1938)
J. Chem. Phys.
, vol.6
, pp. 513
Westheimer, F.H.
1
Kirkwood, J.G.
2
94
0000357114
(1993)
J. Am. Chem. Soc.
, vol.115
, pp. 9563
Lit, E.S.
1
Mallon, F.K.
2
Tsai, H.Y.
3
Roberts, J.D.
4
95
0032560983
(1998)
J. Am. Chem. Soc.
, vol.120
, pp. 9672
Price, D.J.
1
Roberts, J.D.
2
Jorgensen, W.L.
3
96
0004104918
Dover, New York
(1986)
An Introduction to Statistical Thermodynamics
Hill, T.L.
1
97
0003588333
Plenum, New York
(1992)
Statistical Thermodynamics for Chemists and Biochemists
Ben-Naim, A.
1
98
36749107785
(1980)
J. Chem. Phys.
, vol.72
, pp. 2384
Andersen, H.C.
1
99
0001160679
(1984)
Comput. Phys. Rep.
, vol.1
, pp. 299
Evans, D.J.
1
Morriss, G.P.
2
100
84943502952
(1984)
Mol. Phys.
, vol.52
, pp. 255
Nosé, S.
1
101
33750587438
(1984)
J. Chem. Phys.
, vol.81
, pp. 3684
Berendsen, H.J.C.
1
Postma, J.P.M.
2
Van Gunsteren, W.F.
3
DiNola, A.
4
Haak, J.R.
5
102
0001538909
(1985)
Phys. Rev. A
, vol.31
, pp. 1695
Hoover, W.G.
1
103
0003397206
Elsevier, Amsterdam
(1973)
Theory of Electric Polarization
, vol.1
Böttcher, C.J.F.
1
Van Belle, O.C.
2
Bordewijk, P.
3
Rip, A.
4
104
4243137056
(1987)
Phys. Lett. B
, vol.195
, pp. 216
Duane, S.
1
Kennedy, A.D.
2
Pendleton, B.J.
3
Rower, D.
4
105
0027641030
(1993)
Biopolymers
, vol.33
, pp. 1307
Brass, A.
1
Pendleton, B.J.
2
Chen, Y.
3
Robson, R.
4
106
0003421261
Wiley, New York
(1968)
An Introduction to Probability Theory and Its Applications, 3rd ed.
, vol.1
Feller, W.
1
107
0004087349
Springer, Heidelberg
(1960)
Markov Chains with Stationary Transition Probabilities
, vol.1
Chung, K.L.
1
108
77956890234
(1970)
Biometrika
, vol.57
, pp. 97
Hastings, W.K.
1
109
0008819754
(1999)
J. Phys. Chem. A
, vol.103
, pp. 3596
Scott, W.R.P.
1
110
0003544049
VdF: Hochschulverlag AG an der ETH Zürich and BIOMOS b.v., Zürich and Groningen
(1996)
Biomolecular Simulation: The GROMOS96 Manual and User Guide
Van Gunsteren, W.F.
1
111
84990424072
(1984)
Biopolymers
, vol.23
, pp. 1513
Hermans, J.
1
Berendsen, H.J.C.
2
Van Gunsteren, W.F.
3
Postma, J.P.M.
4
112
33646940952
(1977)
J. Comput. Phys.
, vol.23
, pp. 327
Ryckaert, J.-P.
1
Ciccotti, G.
2
Berendsen, H.
3
113
0001158363
(1973)
Mol. Phys.
, vol.26
, pp. 789
Barker, J.A.
1
Watts, R.O.
2
114
4544369164
(1995)
J. Chem. Phys.
, vol.102
, pp. 5451
Tironi, I.G.
1
Sperb, R.
2
Smith, P.E.
3
Van Gunsteren, W.F.
4
115
2242491482
(1994)
J. Chem. Phys.
, vol.100
, pp. 3169
Smith, P.E.
1
Van Gunsteren, W.F.
2
116
84988087911
(1987)
J. Comput. Chem.
, vol.9
, pp. 327
Gilson, M.K.
1
Sharp, K.A.
2
Honig, B.
3
117
0017429069
(1977)
Annu. Rev. Biophys. Bioeng.
, vol.6
, pp. 151
Richards, F.M.
1
118
0003998388
CRC, Boca Raton, FL
(1999)
CRC Handbook of Chemistry and Physics, 80th ed.
Lide, D.R.
1
119
0010305982
The program MCRP is freely available by email request to baptista@itqb.unl.pt
120
5744249209
(1953)
J. Chem. Phys.
, vol.21
, pp. 1087
Metropolis, N.
1
Rosenbluth, A.W.
2
Rosenbluth, M.N.
3
Teller, A.H.
4
Teller, E.
5
121
85052507481
Clarendon, Oxford
(1987)
Computer Simulation of Liquids
Allen, M.P.
1
Tildesley, D.J.
2
122
33748374124
(1978)
J. Chem. Phys.
, vol.68
, pp. 2959
Chandler, D.
1
123
0542421912
(1979)
J. Stat. Phys.
, vol.21
, pp. 1
Ciccotti, G.
1
Jacucci, G.
2
McDonald, I.R.
3
124
0003397206
Elsevier, Amsterdam
(1978)
Theory of Electric Polarization
, vol.2
Böttcher, C.J.F.
1
Bordewijk, P.
2
125
36849122972
(1954)
J. Chem. Phys.
, vol.22
, pp. 1420
Zwanzig, R.W.
1
126
0030134110
(1996)
J. Phys. Chem.
, vol.100
, pp. 9512
Aqvist, J.
1
Hansson, T.
2
127
0242364982
(1996)
J. Chem. Phys.
, vol.105
, pp. 2004
Hummer, G.
1
Szabo, A.
2
128
0033012333
(1999)
Biophys. J.
, vol.75
, pp. 3
Mehler, E.L.
1
Guarnieri, F.
2
129
0032586777
(1999)
Protein Sci.
, vol.8
, pp. 418
Warwicker, J.
1
130
0032568592
(1998)
Proc. Natl. Acad. Sci. U.S.A.
, vol.95
, pp. 6010
Hornemann, S.
1
Glockshuber, R.
2
131
0035798669
(2001)
J. Biol. Chem.
, vol.276
, pp. 40377
Zanusso, G.
1
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