-
2
-
-
0037157317
-
On the Hamiltonian replica exchange method for efficient sampling of biomolecular systems: Application to protein structure prediction
-
DOI 10.1063/1.1472510
-
H. Fukunishi, O. Watanabe, and S. Takada, J. Chem. Phys. 0021-9606 116, 9058 (2002). 10.1063/1.1472510 (Pubitemid 34631453)
-
(2002)
Journal of Chemical Physics
, vol.116
, Issue.20
, pp. 9058-9067
-
-
Fukunishi, H.1
Watanabe, O.2
Takada, S.3
-
4
-
-
0035909921
-
The free energy landscape for β hairpin folding in explicit water
-
DOI 10.1073/pnas.201543998
-
R. Zhou, B. Berne, and R. Germain, Proc. Natl. Acad. Sci. U.S.A. 0027-8424 98, 14931 (2001). 10.1073/pnas.201543998 (Pubitemid 34013947)
-
(2001)
Proceedings of the National Academy of Sciences of the United States of America
, vol.98
, Issue.26
, pp. 14931-14936
-
-
Zhou, R.1
Berne, B.J.2
Germain, R.3
-
5
-
-
31944442794
-
Folding mechanism of β-hairpins studied by replica exchange molecular simulations
-
DOI 10.1002/prot.20813
-
J. Zhang, M. Qin, and W. Wang, Proteins 0887-3585 62, 672 (2006). 10.1002/prot.20813 (Pubitemid 43191254)
-
(2006)
Proteins: Structure, Function and Genetics
, vol.62
, Issue.3
, pp. 672-685
-
-
Zhang, J.1
Qin, M.2
Wang, W.3
-
6
-
-
34548273698
-
Folding Time Predictions from All-atom Replica Exchange Simulations
-
DOI 10.1016/j.jmb.2007.07.010, PII S0022283607009242
-
S. Yang, J. N. Onuchic, A. E. Garcia, and H. Levine, J. Mol. Biol. 0022-2836 372, 756 (2007). 10.1016/j.jmb.2007.07.010 (Pubitemid 47321796)
-
(2007)
Journal of Molecular Biology
, vol.372
, Issue.3
, pp. 756-763
-
-
Yang, S.1
Onuchic, J.N.2
Garcia, A.E.3
Levine, H.4
-
7
-
-
0000666868
-
-
0021-9606 10.1063/1.475210
-
R. Zhou and B. J. Berne, J. Chem. Phys. 0021-9606 107, 9185 (1997). 10.1063/1.475210
-
(1997)
J. Chem. Phys.
, vol.107
, pp. 9185
-
-
Zhou, R.1
Berne, B.J.2
-
8
-
-
0035932735
-
Smart darting Monte Carlo
-
DOI 10.1063/1.1358861
-
I. Andricioaei, J. E. Straub, and A. F. Voter, J. Chem. Phys. 0021-9606 114, 6994 (2001). 10.1063/1.1358861 (Pubitemid 32445479)
-
(2001)
Journal of Chemical Physics
, vol.114
, Issue.16
, pp. 6994-7000
-
-
Andricioaei, I.1
Straub, J.E.2
Voter, A.F.3
-
10
-
-
36049046635
-
An improved replica-exchange sampling method: Temperature intervals with global energy reassignment
-
DOI 10.1063/1.2780152
-
X. Li, C. P. O'Brien, G. Collier, N. A. Vellore, F. Wang, R. A. Latour, D. A. Bruce, and S. J. Stuart, J. Chem. Phys. 0021-9606 127, 164116 (2007). 10.1063/1.2780152 (Pubitemid 350094837)
-
(2007)
Journal of Chemical Physics
, vol.127
, Issue.16
, pp. 164116
-
-
Li, X.1
O'Brien, C.P.2
Collier, G.3
Vellore, N.A.4
Wang, F.5
Latour, R.A.6
Bruce, D.A.7
Stuart, S.J.8
-
11
-
-
34547862465
-
Annealed importance sampling of peptides
-
DOI 10.1063/1.2754267
-
E. Lyman and D. M. Zuckerman, J. Chem. Phys. 0021-9606 127, 065101 (2007). 10.1063/1.2754267 (Pubitemid 47258973)
-
(2007)
Journal of Chemical Physics
, vol.127
, Issue.6
, pp. 065101
-
-
Lyman, E.1
Zuckerman, D.M.2
-
12
-
-
0000888146
-
-
0009-2614 10.1016/S0009-2614(00)00999-4
-
Y. Sugita and Y. Okamoto, Chem. Phys. Lett. 0009-2614 329, 261 (2000). 10.1016/S0009-2614(00)00999-4
-
(2000)
Chem. Phys. Lett.
, vol.329
, pp. 261
-
-
Sugita, Y.1
Okamoto, Y.2
-
13
-
-
4243736249
-
-
1063-651X 10.1103/PhysRevE.63.010902
-
F. Calvo and J. P. K. Doye, Phys. Rev. E 1063-651X 63, 010902 (2000). 10.1103/PhysRevE.63.010902
-
(2000)
Phys. Rev. e
, vol.63
, pp. 010902
-
-
Calvo, F.1
Doye, J.P.K.2
-
14
-
-
0036536011
-
Multicanonical parallel tempering
-
DOI 10.1063/1.1456504
-
R. Faller, Q. Yan, and J. J. de Pablo, J. Chem. Phys. 0021-9606 116, 5419 (2002). 10.1063/1.1456504 (Pubitemid 34435844)
-
(2002)
Journal of Chemical Physics
, vol.116
, Issue.13
, pp. 5419-5423
-
-
Faller, R.1
Yan, Q.2
De Pablo, J.J.3
-
17
-
-
0036495926
-
Generalized parallel sampling
-
DOI 10.1016/S0378-4371(01)00656-2, PII S0378437101006562
-
T. W. Whitfield, L. Bu, and J. E. Straub, Physica A 0378-4371 305, 157 (2002). 10.1016/S0378-4371(01)00656-2 (Pubitemid 34222978)
-
(2002)
Physica A: Statistical Mechanics and its Applications
, vol.305
, Issue.1-2
, pp. 157-171
-
-
Whitfield, T.W.1
Bu, L.2
Straub, J.E.3
-
18
-
-
0141976331
-
-
0031-9007 10.1103/PhysRevLett.91.058305
-
S. Jang, S. Shin, and Y. Pak, Phys. Rev. Lett. 0031-9007 91, 058305 (2003). 10.1103/PhysRevLett.91.058305
-
(2003)
Phys. Rev. Lett.
, vol.91
, pp. 058305
-
-
Jang, S.1
Shin, S.2
Pak, Y.3
-
19
-
-
25444481354
-
Replica exchange with solute tempering: A method for sampling biological systems in explicit water
-
DOI 10.1073/pnas.0506346102
-
P. Liu, B. Kim, R. A. Friesner, and B. J. Berne, Proc. Natl. Acad. Sci. U.S.A. 0027-8424 102, 13749 (2005). 10.1073/pnas.0506346102 (Pubitemid 41377651)
-
(2005)
Proceedings of the National Academy of Sciences of the United States of America
, vol.102
, Issue.39
, pp. 13749-13754
-
-
Liu, P.1
Kim, B.2
Friesner, R.A.3
Berne, B.J.4
-
20
-
-
33749605444
-
Hydrophobic aided replica exchange: An efficient algorithm for protein folding in explicit solvent
-
DOI 10.1021/jp060365r
-
P. Liu, X. Huang, R. Zhou, and B. J. Berne, J. Phys. Chem. B 1089-5647 110, 19018 (2006). 10.1021/jp060365r (Pubitemid 44547290)
-
(2006)
Journal of Physical Chemistry B
, vol.110
, Issue.38
, pp. 19018-19022
-
-
Liu, P.1
Huang, X.2
Zhou, R.3
Berne, B.J.4
-
21
-
-
33846227108
-
Enhanced sampling of peptide and protein conformations using replica exchange simulations with a peptide backbone biasing-potential
-
DOI 10.1002/prot.21258
-
S. Kannan and M. Zacharias, Proteins 0887-3585 66, 697 (2007). 10.1002/prot.21258 (Pubitemid 46106774)
-
(2007)
Proteins: Structure, Function and Genetics
, vol.66
, Issue.3
, pp. 697-706
-
-
Kannan, S.1
Zacharias, M.2
-
22
-
-
33846972360
-
Replica exchange with dynamical scaling
-
DOI 10.1063/1.2431807
-
S. W. Rick, J. Chem. Phys. 0021-9606 126, 054102 (2007). 10.1063/1.2431807 (Pubitemid 46245983)
-
(2007)
Journal of Chemical Physics
, vol.126
, Issue.5
, pp. 054102
-
-
Rick, S.W.1
-
23
-
-
0001692244
-
-
0021-9606 10.1063/1.472109
-
X. Kong and C. L. Brooks III, J. Chem. Phys. 0021-9606 105, 2414 (1996). 10.1063/1.472109
-
(1996)
J. Chem. Phys.
, vol.105
, pp. 2414
-
-
Kong, X.1
Iii, B.L.C.2
-
26
-
-
0000127201
-
Efficient sampling of solvent free energies in polymers
-
DOI 10.1063/1.477379, PII S0021960698510410
-
N. F. A. van der Vegt and W. J. Briels, J. Chem. Phys. 0021-9606 109, 7578 (1998). 10.1063/1.477379 (Pubitemid 128674424)
-
(1998)
Journal of Chemical Physics
, vol.109
, Issue.17
, pp. 7578-7582
-
-
Van Der Vegt, N.F.A.1
Briels, W.J.2
-
27
-
-
0000965020
-
-
0021-9606 10.1063/1.481078
-
S. W. Rick and R. E. Cachau, J. Chem. Phys. 0021-9606 112, 5230 (2000). 10.1063/1.481078
-
(2000)
J. Chem. Phys.
, vol.112
, pp. 5230
-
-
Rick, S.W.1
Cachau, R.E.2
-
28
-
-
0035827113
-
Explicit-solvent molecular dynamics simulation at constant pH: Methodology and application to small amines
-
DOI 10.1063/1.1370959
-
U. Börjesson and P. H. Hünenberger, J. Chem. Phys. 0021-9606 114, 9706 (2001). 10.1063/1.1370959 (Pubitemid 32585970)
-
(2001)
Journal of Chemical Physics
, vol.114
, Issue.22
, pp. 9706-9719
-
-
Borjesson, U.1
Hunenberger, P.H.2
-
29
-
-
4043132337
-
Constant-pH molecular dynamics using continuous titration coordinates
-
DOI 10.1002/prot.20128
-
M. S. Lee, F. R. Salsbury, and C. L. Brooks III, Proteins 0887-3585 56, 738 (2004). 10.1002/prot.20128 (Pubitemid 39063317)
-
(2004)
Proteins: Structure, Function and Genetics
, vol.56
, Issue.4
, pp. 738-752
-
-
Lee, M.S.1
Salsbury Jr., F.R.2
Brooks III, C.L.3
-
30
-
-
23244440384
-
Constant pH molecular dynamics with proton tautomerism
-
DOI 10.1529/biophysj.105.061341
-
J. Khandogin and C. L. Brooks III, Biophys. J. 0006-3495 89, 141 (2005). 10.1529/biophysj.105.061341 (Pubitemid 41098271)
-
(2005)
Biophysical Journal
, vol.89
, Issue.1
, pp. 141-157
-
-
Khandogin, J.1
Brooks III, C.L.2
-
31
-
-
33747625442
-
Efficient and precise solvation free energies via alchemical adiabatic molecular dynamics
-
DOI 10.1063/1.2232082
-
J. B. Abrams, L. Rosso, and M. E. Tuckerman, J. Chem. Phys. 0021-9606 125, 074115 (2006). 10.1063/1.2232082 (Pubitemid 44267416)
-
(2006)
Journal of Chemical Physics
, vol.125
, Issue.7
, pp. 074115
-
-
Abrams, J.B.1
Rosso, L.2
Tuckerman, M.E.3
-
32
-
-
15544384111
-
On the efficiency of exchange in parallel tempering Monte Carlo simulations
-
DOI 10.1021/jp045073+
-
C. Predescu, M. Predescu, and C. V. Ciobanu, J. Phys. Chem. B 1089-5647 109, 4189 (2005). 10.1021/jp045073+ (Pubitemid 40402302)
-
(2005)
Journal of Physical Chemistry B
, vol.109
, Issue.9
, pp. 4189-4196
-
-
Predescu, C.1
Predescu, M.2
Ciobanu, C.V.3
-
34
-
-
22944453404
-
Optimal allocation of replicas in parallel tempering simulations
-
DOI 10.1063/1.1831273, 024111
-
N. Rathore, M. Chopra, and J. J. de Pablo, J. Chem. Phys. 0021-9606 122, 024111 (2005). 10.1063/1.1831273 (Pubitemid 41047689)
-
(2005)
Journal of Chemical Physics
, vol.122
, Issue.2
, pp. 1-8
-
-
Rathore, N.1
Chopra, M.2
De Pablo, J.J.3
-
35
-
-
20844439932
-
Selection of temperature intervals for parallel-tempering simulations
-
DOI 10.1063/1.1917749, 206101
-
A. Kone and D. A. Kofke, J. Chem. Phys. 0021-9606 122, 206101 (2005). 10.1063/1.1917749 (Pubitemid 40858531)
-
(2005)
Journal of Chemical Physics
, vol.122
, Issue.20
, pp. 1-2
-
-
Kone, A.1
Kofke, D.A.2
-
36
-
-
0035826776
-
Tryptophan zippers: Stable, monomeric β-hairpins
-
DOI 10.1073/pnas.091100898
-
A. G. Cochran, N. J. Skelton, and M. A. Starovasnik, Proc. Natl. Acad. Sci. U.S.A. 0027-8424 98, 5578 (2001). 10.1073/pnas.091100898 (Pubitemid 32435684)
-
(2001)
Proceedings of the National Academy of Sciences of the United States of America
, vol.98
, Issue.10
, pp. 5578-5583
-
-
Cochran, A.G.1
Skelton, N.J.2
Starovasnik, M.A.3
-
37
-
-
5744249209
-
-
0021-9606 10.1063/1.1699114
-
N. Metropolis, A. Rosenbluth, M. Rosenbluth, A. Teller, and E. Teller, J. Chem. Phys. 0021-9606 21, 1087 (1953). 10.1063/1.1699114
-
(1953)
J. Chem. Phys.
, vol.21
, pp. 1087
-
-
Metropolis, N.1
Rosenbluth, A.2
Rosenbluth, M.3
Teller, A.4
Teller, E.5
-
38
-
-
0029912748
-
Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids
-
DOI 10.1021/ja9621760, PII S0002786396021762
-
W. L. Jorgensen, D. S. Maxwell, and J. Tirado-Rives, J. Am. Chem. Soc. 0002-7863 118, 11225 (1996). 10.1021/ja9621760 (Pubitemid 26399746)
-
(1996)
Journal of the American Chemical Society
, vol.118
, Issue.45
, pp. 11225-11236
-
-
Jorgensen, W.L.1
Maxwell, D.S.2
Tirado-Rives, J.3
-
39
-
-
0035913529
-
Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides
-
DOI 10.1021/jp003919d
-
G. A. Kaminski, R. A. Friesner, J. Tirado-Rives, and W. L. Jorgensen, J. Phys. Chem. B 1089-5647 105, 6474 (2001). 10.1021/jp003919d (Pubitemid 35339015)
-
(2001)
Journal of Physical Chemistry B
, vol.105
, Issue.28
, pp. 6474-6487
-
-
Kaminski, G.A.1
Friesner, R.A.2
Tirado-Rives, J.3
Jorgensen, W.L.4
-
40
-
-
0004016501
-
-
0021-9606 10.1063/1.445869
-
W. L. Jorgensen, J. Chandrasekhar, J. D. Madura, R. W. Impey, and M. L. Klein, J. Chem. Phys. 0021-9606 79, 926 (1983). 10.1063/1.445869
-
(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
-
41
-
-
0001616080
-
-
0009-2614 10.1016/S0009-2614(99)01123-9
-
Y. Sugita and Y. Okamoto, Chem. Phys. Lett. 0009-2614 314, 141 (1999). 10.1016/S0009-2614(99)01123-9
-
(1999)
Chem. Phys. Lett.
, vol.314
, pp. 141
-
-
Sugita, Y.1
Okamoto, Y.2
-
42
-
-
0001398008
-
-
0192-8651 10.1002/1096-987X(200009)21:12<1049::AID-JCC33.0.CO;2-F
-
J. Wang, P. Cieplak, and P. Kollman, J. Comput. Chem. 0192-8651 21, 1049 (2000). 10.1002/1096-987X(200009)21:12<1049::AID-JCC33.0.CO;2-F
-
(2000)
J. Comput. Chem.
, vol.21
, pp. 1049
-
-
Wang, J.1
Cieplak, P.2
Kollman, P.3
-
43
-
-
33748518255
-
Comparison of multiple amber force fields and development of improved protein backbone parameters
-
DOI 10.1002/prot.21123
-
V. Hornak, R. Abel, A. Okur, B. Strockbine, A. Roitberg, and C. Simmerling, Proteins 0887-3585 65, 712 (2006). 10.1002/prot.21123 (Pubitemid 44583220)
-
(2006)
Proteins: Structure, Function and Genetics
, vol.65
, Issue.3
, pp. 712-725
-
-
Hornak, V.1
Abel, R.2
Okur, A.3
Strockbine, B.4
Roitberg, A.5
Simmerling, C.6
-
44
-
-
70449334698
-
-
AMBER9, University of California, San Francisco.
-
D. A. Case, T. A. Darden, T. E. Cheatham III, C. L. Simmerling, J. Wang, R. E. Duke, R. Luo, K. M. Merz, D. A. Pearlman, M. Crowley, AMBER9, University of California, San Francisco, 2006.
-
(2006)
-
-
Case, D.A.1
Darden, T.A.2
Iii, C.E.T.3
Simmerling, C.L.4
Wang, J.5
Duke, R.E.6
Luo, R.7
Merz, K.M.8
Pearlman, D.A.9
Crowley, M.10
-
45
-
-
70449349016
-
-
In Fig. 1 of Ref., the x-axis is incorrectly labeled. It should read 0.02, 0.04, 0.06, 0.08, and 0.10.
-
In Fig. 1 of Ref., the x-axis is incorrectly labeled. It should read 0.02, 0.04, 0.06, 0.08, and 0.10.
-
-
-
-
46
-
-
0035333238
-
-
1063-651X 10.1103/PhysRevE.63.056701
-
S. B. Opps and J. Schofield, Phys. Rev. E 1063-651X 63, 056701 (2001). 10.1103/PhysRevE.63.056701
-
(2001)
Phys. Rev. e
, vol.63
, pp. 056701
-
-
Opps, S.B.1
Schofield, J.2
-
47
-
-
33645722974
-
-
0021-9606 10.1063/1.2056540
-
W. Zhang, C. Wu, and Y. Duan, J. Chem. Phys. 0021-9606 123, 154105 (2005). 10.1063/1.2056540
-
(2005)
J. Chem. Phys.
, vol.123
, pp. 154105
-
-
Zhang, W.1
Wu, C.2
Duan, Y.3
-
48
-
-
33846106377
-
Convergence and sampling efficiency in replica exchange simulations of peptide folding in explicit solvent
-
DOI 10.1063/1.2404954
-
X. Periole and A. E. Mark, J. Chem. Phys. 0021-9606 126, 014903 (2007). 10.1063/1.2404954 (Pubitemid 46068420)
-
(2007)
Journal of Chemical Physics
, vol.126
, Issue.1
, pp. 014903
-
-
Periole, X.1
Mark, A.E.2
-
51
-
-
70449331854
-
-
L is 0<φ<130 and -60<ψ<90; and C 7a x is 0<φ<130 and ψ<-60 or ψ90.
-
L is 0<φ<130 and -60<ψ<90; and C 7a x is 0<φ<130 and ψ<-60 or ψ90.sssssssssss
-
-
-
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