-
1
-
-
2942567954
-
Describing protein folding kinetics by molecular dynamics simulations. Theory
-
Swope, W.C., J.W. Pitera, and F. Suits, Describing protein folding kinetics by molecular dynamics simulations. Theory. Journal of Physical Chemistry B, 2004. 108(21): p. 6571-6581.
-
(2004)
Journal of Physical Chemistry B
, vol.108
, Issue.21
, pp. 6571-6581
-
-
Swope, W.C.1
Pitera, J.W.2
Suits, F.3
-
2
-
-
41549086176
-
Peptide folding kinetics from replica exchange molecular dynamics
-
Buchete, N.V. and G. Hummer, Peptide folding kinetics from replica exchange molecular dynamics. Phys Rev E Stat Nonlin Soft Matter Phys, 2008. 77(3 Pt 1): p. 030902.
-
(2008)
Phys Rev e Stat Nonlin Soft Matter Phys
, vol.77
, Issue.3 PART 1
, pp. 030902
-
-
Buchete, N.V.1
Hummer, G.2
-
3
-
-
17444389688
-
Coarse master equation from Bayesian analysis of replica molecular dynamics simulations
-
Sriraman, S., I.G. Kevrekidis, and G. Hummer, Coarse master equation from Bayesian analysis of replica molecular dynamics simulations. J Phys Chem B, 2005. 109(14): p. 6479-84.
-
(2005)
J Phys Chem B
, vol.109
, Issue.14
, pp. 6479-6484
-
-
Sriraman, S.1
Kevrekidis, I.G.2
Hummer, G.3
-
4
-
-
42149175435
-
Transition networks for modeling the kinetics of conformational change in macromolecules
-
Noe, F. and S. Fischer, Transition networks for modeling the kinetics of conformational change in macromolecules. Curr Opin Struct Biol, 2008. 18(2): p. 154-62.
-
(2008)
Curr Opin Struct Biol
, vol.18
, Issue.2
, pp. 154-162
-
-
Noe, F.1
Fischer, S.2
-
5
-
-
3142707288
-
Using path sampling to build better Markovian state models: Predicting the folding rate and mechanism of a tryptophan zipper beta hairpin
-
Singhal, N., C.D. Snow, and V.S. Pande, Using path sampling to build better Markovian state models: Predicting the folding rate and mechanism of a tryptophan zipper beta hairpin. Journal of Chemical Physics, 2004. 121(1): p. 415-425.
-
(2004)
Journal of Chemical Physics
, vol.121
, Issue.1
, pp. 415-425
-
-
Singhal, N.1
Snow, C.D.2
Pande, V.S.3
-
6
-
-
63449118443
-
Using generalized ensemble simulations and Markov state models to identify conformational states
-
Bowman, G.R., X. Huang, and V.S. Pande, Using generalized ensemble simulations and Markov state models to identify conformational states. Methods, 2009.
-
(2009)
Methods
-
-
Bowman, G.R.1
Huang, X.2
Pande, V.S.3
-
7
-
-
34247338100
-
Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics
-
Chodera, J.D., et al., Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics. J Chem Phys, 2007. 126(15): p. 155101.
-
(2007)
J Chem Phys
, vol.126
, Issue.15
, pp. 155101
-
-
Chodera, J.D.1
-
8
-
-
39449131104
-
Coarse-grained simulation: A high-throughput computational approach to membrane proteins
-
Sansom, M.S., K.A. Scott, and P.J. Bond, Coarse-grained simulation: a high-throughput computational approach to membrane proteins. Biochem Soc Trans, 2008. 36(Pt 1): p. 27-32.
-
(2008)
Biochem Soc Trans
, vol.36
, Issue.PART 1
, pp. 27-32
-
-
Sansom, M.S.1
Scott, K.A.2
Bond, P.J.3
-
9
-
-
34547474332
-
The MARTINI force field: Coarse grained model for biomolecular simulations
-
Marrink, S.J., et al., The MARTINI force field: coarse grained model for biomolecular simulations. J Phys Chem B, 2007. 111(27): p. 7812-24.
-
(2007)
J Phys Chem B
, vol.111
, Issue.27
, pp. 7812-7824
-
-
Marrink, S.J.1
-
10
-
-
0035812110
-
Effect of undulations on surface tension in simulated bilayers
-
Marrink, S.J. and A.E. Mark, Effect of undulations on surface tension in simulated bilayers. Journal of Physical Chemistry B, 2001. 105(26): p. 6122-6127.
-
(2001)
Journal of Physical Chemistry B
, vol.105
, Issue.26
, pp. 6122-6127
-
-
Marrink, S.J.1
Mark, A.E.2
-
11
-
-
4444293963
-
Simulation of domain formation in DLPC-DSPC mixed bilayers
-
Faller, R. and S.J. Marrink, Simulation of domain formation in DLPC-DSPC mixed bilayers. Langmuir, 2004. 20(18): p. 7686-93.
-
(2004)
Langmuir
, vol.20
, Issue.18
, pp. 7686-7693
-
-
Faller, R.1
Marrink, S.J.2
-
12
-
-
19744367689
-
Simulation of gel phase formation and melting in lipid bilayers using a coarse grained model
-
Marrink, S.J., J. Risselada, and A.E. Mark, Simulation of gel phase formation and melting in lipid bilayers using a coarse grained model. Chemistry and Physics of Lipids, 2005.
-
(2005)
Chemistry and Physics of Lipids
-
-
Marrink, S.J.1
Risselada, J.2
Mark, A.E.3
-
13
-
-
33644929350
-
Multiscale coarse graining of liquid-state systems
-
Izvekov, S. and G.A. Voth, Multiscale coarse graining of liquid-state systems. J Chem Phys, 2005. 123(13): p. 134105.
-
(2005)
J Chem Phys
, vol.123
, Issue.13
, pp. 134105
-
-
Izvekov, S.1
Voth, G.A.2
-
14
-
-
25844472744
-
Multi-scale modeling of phase separation in mixed lipid bilayers
-
Shi, Q. and G.A. Voth, Multi-scale modeling of phase separation in mixed lipid bilayers. Biophys J, 2005. 89(4): p. 2385-94.
-
(2005)
Biophys J
, vol.89
, Issue.4
, pp. 2385-2394
-
-
Shi, Q.1
Voth, G.A.2
-
15
-
-
16344369596
-
Mesoscopic lateral diffusion in lipid bilayers
-
Ayton, G.S. and G.A. Voth, Mesoscopic lateral diffusion in lipid bilayers. Biophys J, 2004. 87(5): p. 3299-311.
-
(2004)
Biophys J
, vol.87
, Issue.5
, pp. 3299-3311
-
-
Ayton, G.S.1
Voth, G.A.2
-
16
-
-
33747064957
-
Ensemble molecular dynamics yields sub-millisecond kinetics and intermediates of membrane fusion
-
Kasson, P.M., et al., Ensemble molecular dynamics yields sub-millisecond kinetics and intermediates of membrane fusion. Proc Natl Acad Sci U S A, 2006. 103(32): p. 11916-21.
-
(2006)
Proc Natl Acad Sci U S A
, vol.103
, Issue.32
, pp. 11916-11921
-
-
Kasson, P.M.1
-
17
-
-
33644644163
-
Insertion and assembly of membrane proteins via simulation
-
Bond, P.J. and M.S. Sansom, Insertion and assembly of membrane proteins via simulation. J Am Chem Soc, 2006. 128(8): p. 2697-704.
-
(2006)
J Am Chem Soc
, vol.128
, Issue.8
, pp. 2697-2704
-
-
Bond, P.J.1
Sansom, M.S.2
-
18
-
-
54849405417
-
Self-assembly of a simple membrane protein: Coarse-grained molecular dynamics simulations of the influenza M2 channel
-
Carpenter, T., et al., Self-assembly of a simple membrane protein: coarse-grained molecular dynamics simulations of the influenza M2 channel. Biophys J, 2008. 95(8): p. 3790-801.
-
(2008)
Biophys J
, vol.95
, Issue.8
, pp. 3790-3801
-
-
Carpenter, T.1
-
19
-
-
34247895641
-
Membrane remodeling from N-BAR domain interactions: Insights from multi-scale simulation
-
Ayton, G.S., P.D. Blood, and G.A. Voth, Membrane remodeling from N-BAR domain interactions: insights from multi-scale simulation. Biophys J, 2007. 92(10): p. 3595-602.
-
(2007)
Biophys J
, vol.92
, Issue.10
, pp. 3595-3602
-
-
Ayton, G.S.1
Blood, P.D.2
Voth, G.A.3
-
20
-
-
32044451318
-
Validation of Markov state models using Shannon's entropy
-
Park, S. and V.S. Pande, Validation of Markov state models using Shannon's entropy. J Chem Phys, 2006. 124(5): p. 54118.
-
(2006)
J Chem Phys
, vol.124
, Issue.5
, pp. 54118
-
-
Park, S.1
Pande, V.S.2
-
21
-
-
43149103416
-
Mechanosensitive membrane channels in action
-
Yefimov, S., et al., Mechanosensitive membrane channels in action. Biophys J, 2008. 94(8): p. 2994-3002.
-
(2008)
Biophys J
, vol.94
, Issue.8
, pp. 2994-3002
-
-
Yefimov, S.1
-
22
-
-
66649132042
-
The structure of a cytolytic alpha-helical toxin pore reveals its assembly mechanism
-
Mueller, M., et al., The structure of a cytolytic alpha-helical toxin pore reveals its assembly mechanism. Nature, 2009. 459(7247): p. 726-30.
-
(2009)
Nature
, vol.459
, Issue.7247
, pp. 726-730
-
-
Mueller, M.1
-
23
-
-
34547341247
-
Calculation of the distribution of eigenvalues and eigenvectors in Markovian state models for molecular dynamics
-
Hinrichs, N.S. and V.S. Pande, Calculation of the distribution of eigenvalues and eigenvectors in Markovian state models for molecular dynamics. The Journal of chemical physics, 2007. 126(24): p. 244101.
-
(2007)
The Journal of Chemical Physics
, vol.126
, Issue.24
, pp. 244101
-
-
Hinrichs, N.S.1
Pande, V.S.2
-
24
-
-
46249092554
-
GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation
-
Hess, B., et al., GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation. Journal of Chemical Theory and Computation, 2008. 4: p. 435-447.
-
(2008)
Journal of Chemical Theory and Computation
, vol.4
, pp. 435-447
-
-
Hess, B.1
-
25
-
-
33644893631
-
Coarse grained protein-lipid model with application to lipoprotein particles
-
Shih, A.Y., et al., Coarse grained protein-lipid model with application to lipoprotein particles. J Phys Chem B, 2006. 110(8): p. 3674-84.
-
(2006)
J Phys Chem B
, vol.110
, Issue.8
, pp. 3674-3684
-
-
Shih, A.Y.1
-
26
-
-
1642485164
-
Coarse grained model for semiquantitative lipid simulations
-
Marrink, S.J., A.H. de Vries, and A.E. Mark, Coarse grained model for semiquantitative lipid simulations. Journal of Physical Chemistry B, 2004. 108(2): p. 750-760.
-
(2004)
Journal of Physical Chemistry B
, vol.108
, Issue.2
, pp. 750-760
-
-
Marrink, S.J.1
De Vries, A.H.2
Mark, A.E.3
-
27
-
-
58149181485
-
Lipids on the move: Simulations of membrane pores, domains, stalks and curves
-
Marrink, S.J., A.H. de Vries, and D.P. Tieleman, Lipids on the move: simulations of membrane pores, domains, stalks and curves. Biochim Biophys Acta, 2009. 1788(1): p. 149-68.
-
(2009)
Biochim Biophys Acta
, vol.1788
, Issue.1
, pp. 149-168
-
-
Marrink, S.J.1
De Vries, A.H.2
Tieleman, D.P.3
|