-
1
-
-
35949020425
-
Replica Monte-Carlo simulation of spin-glasses
-
Swendsen, R. H.; Wang, J. S. Replica Monte-Carlo simulation of spin-glasses Phys. Rev. Lett. 1986, 57 (21) 2607-2609
-
(1986)
Phys. Rev. Lett.
, vol.57
, Issue.21
, pp. 2607-2609
-
-
Swendsen, R.H.1
Wang, J.S.2
-
2
-
-
0030516672
-
Exchange Monte Carlo Method and Application to Spin Glass Simulations
-
Hukushima, K.; Nemoto, K. Exchange Monte Carlo method and application to spin glass simulations J. Phys. Soc. Jpn. 1996, 65 (6) 1604-1608 (Pubitemid 126456584)
-
(1996)
Journal of the Physical Society of Japan
, vol.65
, Issue.6
, pp. 1604-1608
-
-
Hukushima, K.1
Nemoto, K.2
-
3
-
-
0001616080
-
Replica-exchange molecular dynamics method for protein folding
-
Sugita, Y.; Okamoto, Y. Replica-exchange molecular dynamics method for protein folding Chem. Phys. Lett. 1999, 314 (1-2) 141-151
-
(1999)
Chem. Phys. Lett.
, vol.314
, Issue.12
, pp. 141-151
-
-
Sugita, Y.1
Okamoto, Y.2
-
5
-
-
0344824394
-
Trp-cage: Folding free energy landscape in explicit water
-
Zhou, R. Trp-cage: folding free energy landscape in explicit water Proc. Natl. Acad. Sci. U.S.A. 2003, 100 (23) 13280-13285
-
(2003)
Proc. Natl. Acad. Sci. U.S.A.
, vol.100
, Issue.23
, pp. 13280-13285
-
-
Zhou, R.1
-
6
-
-
0345133287
-
Folding a protein in a computer: An atomic description of the folding/unfolding of protein A
-
Garcia, A. E.; Onuchic, J. N. Folding a protein in a computer: An atomic description of the folding/unfolding of protein A Proc. Natl. Acad. Sci. U.S.A. 2003, 100 (24) 13898-13903
-
(2003)
Proc. Natl. Acad. Sci. U.S.A.
, vol.100
, Issue.24
, pp. 13898-13903
-
-
Garcia, A.E.1
Onuchic, J.N.2
-
7
-
-
70350025164
-
Tryptophan conformations associated with partial unfolding in ribonuclease T1
-
Moors, S. L. C.; Jonckheer, A.; De Maeyer, M.; Engelborghs, Y.; Ceulemans, A. Tryptophan conformations associated with partial unfolding in ribonuclease T1 Biophys. J. 2009, 97 (6) 1778-1786
-
(2009)
Biophys. J.
, vol.97
, Issue.6
, pp. 1778-1786
-
-
Moors, S.L.C.1
Jonckheer, A.2
De Maeyer, M.3
Engelborghs, Y.4
Ceulemans, A.5
-
8
-
-
0037157317
-
On the Hamiltonian replica exchange method for efficient sampling of biomolecular systems: Application to protein structure prediction
-
Fukunishi, H.; Watanabe, O.; Takada, S. On the Hamiltonian replica exchange method for efficient sampling of biomolecular systems: Application to protein structure prediction J. Chem. Phys. 2002, 116 (20) 9058-9067
-
(2002)
J. Chem. Phys.
, vol.116
, Issue.20
, pp. 9058-9067
-
-
Fukunishi, H.1
Watanabe, O.2
Takada, S.3
-
9
-
-
28844454252
-
Parallel tempering: Theory, applications, and new perspectives
-
Earl, D. J.; Deem, M. W. Parallel tempering: Theory, applications, and new perspectives Phys. Chem. Chem. Phys. 2005, 7 (23) 3910-3916
-
(2005)
Phys. Chem. Chem. Phys.
, vol.7
, Issue.23
, pp. 3910-3916
-
-
Earl, D.J.1
Deem, M.W.2
-
10
-
-
58149131549
-
How is cis-trans isomerization controlled in Dronpa mutants- A replica exchange molecular dynamics study
-
Moors, S. L. C.; Michielssens, S.; Flors, C.; Dedecker, P.; Hofkens, J.; Ceulemans, A. How is cis-trans isomerization controlled in Dronpa mutants- A replica exchange molecular dynamics study J. Chem. Theory Comput. 2008, 4 (6) 1012-1020
-
(2008)
J. Chem. Theory Comput.
, vol.4
, Issue.6
, pp. 1012-1020
-
-
Moors, S.L.C.1
Michielssens, S.2
Flors, C.3
Dedecker, P.4
Hofkens, J.5
Ceulemans, A.6
-
11
-
-
33749605444
-
Hydrophobic aided replica exchange: An efficient algorithm for protein folding in explicit solvent
-
Liu, P.; Huang, X. H.; Zhou, R. H.; Berne, B. J. Hydrophobic aided replica exchange: An efficient algorithm for protein folding in explicit solvent J. Phys. Chem. B 2006, 110 (38) 19018-19022
-
(2006)
J. Phys. Chem. B
, vol.110
, Issue.38
, pp. 19018-19022
-
-
Liu, P.1
Huang, X.H.2
Zhou, R.H.3
Berne, B.J.4
-
12
-
-
42149182885
-
Hamiltonian replica exchange molecular dynamics using soft-core interactions
-
Hritz, J.; Oostenbrink, C. Hamiltonian replica exchange molecular dynamics using soft-core interactions J. Chem. Phys. 2008, 128 (14) 144121
-
(2008)
J. Chem. Phys.
, vol.128
, Issue.14
, pp. 144121
-
-
Hritz, J.1
Oostenbrink, C.2
-
13
-
-
33846227108
-
Enhanced sampling of peptide and protein conformations using replica exchange simulations with a peptide backbone biasing-potential
-
Kannan, S.; Zacharias, M. Enhanced sampling of peptide and protein conformations using replica exchange simulations with a peptide backbone biasing-potential Proteins 2007, 66 (3) 697-706
-
(2007)
Proteins
, vol.66
, Issue.3
, pp. 697-706
-
-
Kannan, S.1
Zacharias, M.2
-
14
-
-
58149145248
-
Combining elastic network analysis and molecular dynamics simulations by hamiltonian replica exchange
-
Zacharias, M. Combining elastic network analysis and molecular dynamics simulations by hamiltonian replica exchange J. Chem. Theory Comput. 2008, 4 (3) 477-487
-
(2008)
J. Chem. Theory Comput.
, vol.4
, Issue.3
, pp. 477-487
-
-
Zacharias, M.1
-
15
-
-
25444481354
-
Replica exchange with solute tempering: A method for sampling biological systems in explicit water
-
Liu, P.; Kim, B.; Friesner, R. A.; Berne, B. J. Replica exchange with solute tempering: A method for sampling biological systems in explicit water Proc. Natl. Acad. Sci. U.S.A. 2005, 102 (39) 13749-13754
-
(2005)
Proc. Natl. Acad. Sci. U.S.A.
, vol.102
, Issue.39
, pp. 13749-13754
-
-
Liu, P.1
Kim, B.2
Friesner, R.A.3
Berne, B.J.4
-
16
-
-
0035427398
-
Protein flexibility predictions using graph theory
-
Jacobs, D. J.; Rader, A. J.; Kuhn, L. A.; Thorpe, M. F. Protein flexibility predictions using graph theory Proteins 2001, 44 (2) 150-165
-
(2001)
Proteins
, vol.44
, Issue.2
, pp. 150-165
-
-
Jacobs, D.J.1
Rader, A.J.2
Kuhn, L.A.3
Thorpe, M.F.4
-
17
-
-
0242663237
-
A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations
-
Duan, Y.; Wu, C.; Chowdhury, S.; Lee, M. C.; Xiong, G. M.; Zhang, W.; Yang, R.; Cieplak, P.; Luo, R.; Lee, T.; Caldwell, J.; Wang, J. M.; Kollman, P. A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations J. Comput. Chem. 2003, 24 (16) 1999-2012
-
(2003)
J. Comput. Chem.
, vol.24
, Issue.16
, pp. 1999-2012
-
-
Duan, Y.1
Wu, C.2
Chowdhury, S.3
Lee, M.C.4
Xiong, G.M.5
Zhang, W.6
Yang, R.7
Cieplak, P.8
Luo, R.9
Lee, T.10
Caldwell, J.11
Wang, J.M.12
Kollman, P.13
-
18
-
-
46249092554
-
GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation
-
Hess, B.; Kutzner, C.; van der Spoel, D.; Lindahl, E. GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation J. Chem. Theory Comput. 2008, 4 (3) 435-447
-
(2008)
J. Chem. Theory Comput.
, vol.4
, Issue.3
, pp. 435-447
-
-
Hess, B.1
Kutzner, C.2
Van Der Spoel, D.3
Lindahl, E.4
-
19
-
-
33645961739
-
A smooth particle mesh Ewald method
-
Essmann, U.; Perera, L.; Berkowitz, M. L.; Darden, T.; Lee, H.; Pedersen, L. G. A smooth particle mesh Ewald method J. Chem. Phys. 1995, 103 (19) 8577-8593
-
(1995)
J. Chem. Phys.
, vol.103
, Issue.19
, pp. 8577-8593
-
-
Essmann, U.1
Perera, L.2
Berkowitz, M.L.3
Darden, T.4
Lee, H.5
Pedersen, L.G.6
-
20
-
-
38749123962
-
P-LINCS: A parallel linear constraint solver for molecular simulation
-
Hess, B. P-LINCS: A parallel linear constraint solver for molecular simulation J. Chem. Theory Comput. 2008, 4 (1) 116-122
-
(2008)
J. Chem. Theory Comput.
, vol.4
, Issue.1
, pp. 116-122
-
-
Hess, B.1
-
21
-
-
33846086933
-
Canonical sampling through velocity rescaling
-
(014101
-
Bussi, G.; Donadio, D.; Parrinello, M. Canonical sampling through velocity rescaling J. Chem. Phys. 2007, 126 (1 014101
-
(2007)
J. Chem. Phys.
, vol.126
, Issue.1
-
-
Bussi, G.1
Donadio, D.2
Parrinello, M.3
-
22
-
-
23144457576
-
H++: A server for estimating pK(a)s and adding missing hydrogens to macromolecules
-
Gordon, J. C.; Myers, J. B.; Folta, T.; Shoja, V.; Heath, L. S.; Onufriev, A. H++: a server for estimating pK(a)s and adding missing hydrogens to macromolecules Nucleic Acids Res. 2005, 33 (Web Server issue) W368-W371
-
(2005)
Nucleic Acids Res.
, vol.33
, Issue.WEB SERVER ISSUE
-
-
Gordon, J.C.1
Myers, J.B.2
Folta, T.3
Shoja, V.4
Heath, L.S.5
Onufriev, A.6
-
23
-
-
0032080528
-
Domain motions in bacteriophage T4 lysozyme: A comparison between molecular dynamics and crystallographic data
-
de Groot, B. L.; Hayward, S.; van Aalten, D. M.; Amadei, A.; Berendsen, H. J. Domain motions in bacteriophage T4 lysozyme: A comparison between molecular dynamics and crystallographic data Proteins 1998, 31 (2) 116-127
-
(1998)
Proteins
, vol.31
, Issue.2
, pp. 116-127
-
-
De Groot, B.L.1
Hayward, S.2
Van Aalten, D.M.3
Amadei, A.4
Berendsen, H.J.5
-
24
-
-
0029150760
-
Protein flexibility and adaptability seen in 25 crystalforms of T4 lysozyme
-
Zhang, X. J.; Wozniak, J. A.; Matthews, B. W. Protein flexibility and adaptability seen in 25 crystalforms of T4 lysozyme J. Mol. Biol. 1995, 250 (4) 527-552
-
(1995)
J. Mol. Biol.
, vol.250
, Issue.4
, pp. 527-552
-
-
Zhang, X.J.1
Wozniak, J.A.2
Matthews, B.W.3
-
25
-
-
1842326248
-
Conformation of T4 lysozyme in solution. Hinge-bending motion and the substrate-induced conformational transition studied by site-directed spin labeling
-
Mchaourab, H. S.; Oh, K. J.; Fang, C. J.; Hubbell, W. L. Conformation of T4 lysozyme in solution. Hinge-bending motion and the substrate-induced conformational transition studied by site-directed spin labeling Biochemistry 1997, 36 (2) 307-316
-
(1997)
Biochemistry
, vol.36
, Issue.2
, pp. 307-316
-
-
McHaourab, H.S.1
Oh, K.J.2
Fang, C.J.3
Hubbell, W.L.4
-
26
-
-
35748982413
-
Geometry-based sampling of conformational transitions in proteins
-
Seeliger, D.; Haas, J.; de Groot, B. L. Geometry-based sampling of conformational transitions in proteins Structure 2007, 15 (11) 1482-1492
-
(2007)
Structure
, vol.15
, Issue.11
, pp. 1482-1492
-
-
Seeliger, D.1
Haas, J.2
De Groot, B.L.3
-
27
-
-
34249781419
-
Replica exchange with solute tempering: Efficiency in large scale systems
-
Huang, X. H.; Hagen, M.; Kim, B.; Friesner, R. A.; Zhou, R. H.; Berne, B. J. Replica exchange with solute tempering: Efficiency in large scale systems J. Phys. Chem. B 2007, 111 (19) 5405-5410
-
(2007)
J. Phys. Chem. B
, vol.111
, Issue.19
, pp. 5405-5410
-
-
Huang, X.H.1
Hagen, M.2
Kim, B.3
Friesner, R.A.4
Zhou, R.H.5
Berne, B.J.6
-
30
-
-
0034972906
-
What is the average conformation of bacteriophage T4 lysozyme in solution- A domain orientation study using dipolar couplings measured by solution NMR
-
Goto, N. K.; Skrynnikov, N. R.; Dahlquist, F. W.; Kay, L. E. What is the average conformation of bacteriophage T4 lysozyme in solution- A domain orientation study using dipolar couplings measured by solution NMR J. Mol. Biol. 2001, 308 (4) 745-764
-
(2001)
J. Mol. Biol.
, vol.308
, Issue.4
, pp. 745-764
-
-
Goto, N.K.1
Skrynnikov, N.R.2
Dahlquist, F.W.3
Kay, L.E.4
-
31
-
-
33748518255
-
Comparison of multiple amber force fields and development of improved protein backbone parameters
-
Hornak, V.; Abel, R.; Okur, A.; Strockbine, B.; Roitberg, A.; Simmerling, C. Comparison of multiple amber force fields and development of improved protein backbone parameters Proteins 2006, 65 (3) 712-725
-
(2006)
Proteins
, 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
-
32
-
-
34548273698
-
Folding time predictions from all-atom replica exchange simulations
-
Yang, S.; Onuchic, J. N.; Garcia, A. E.; Levine, H. Folding time predictions from all-atom replica exchange simulations J. Mol. Biol. 2007, 372 (3) 756-763
-
(2007)
J. Mol. Biol.
, vol.372
, Issue.3
, pp. 756-763
-
-
Yang, S.1
Onuchic, J.N.2
Garcia, A.E.3
Levine, H.4
|