-
3
-
-
0004168443
-
-
(Dover Publications, New York)
-
H. Lamb, Hydrodynamics (Dover Publications, New York, 1993).
-
(1993)
Hydrodynamics
-
-
Lamb, H.1
-
6
-
-
4243606192
-
-
10.1103/PhysRevLett.55.2471
-
R. Car and M. Parrinello, Phys. Rev. Lett. 55, 2471 (1985). 10.1103/PhysRevLett.55.2471
-
(1985)
Phys. Rev. Lett.
, vol.55
, pp. 2471
-
-
Car, R.1
Parrinello, M.2
-
8
-
-
36248975150
-
-
version 4.5.4
-
D. van der Spoel, E. Lindahl, B. Hess, A. R. van Buuren, E. Apol, P. J. Meulenhoff, D. P. Tieleman, A. L. T. M. Sijbers, K. A. Feenstra, R. van Drunen, and H. J. C. Berendsen, Gromacs User Manual, version 4.5.4 (www.gromacs.org, 2010).
-
(2010)
Gromacs User Manual
-
-
Van Der Spoel, D.1
Lindahl, E.2
Hess, B.3
Van Buuren, A.R.4
Apol, E.5
Meulenhoff, P.J.6
Tieleman, D.P.7
Sijbers, A.L.T.M.8
Feenstra, K.A.9
Van Drunen, R.10
Berendsen, H.J.C.11
-
9
-
-
0036725277
-
Molecular dynamics simulations of biomolecules
-
DOI 10.1038/nsb0902-646
-
M. Karplus and J. A. McCammon, Nat. Struct. Mol. Biol. 9, 646 (2002). 10.1038/nsb0902-646 (Pubitemid 34977295)
-
(2002)
Nature Structural Biology
, vol.9
, Issue.9
, pp. 646-652
-
-
Karplus, M.1
McCammon, J.A.2
-
12
-
-
37749031058
-
-
10.1038/nphys788
-
L. Larini, A. Ottochian, C. De Michele, and D. Leporini, Nat. Phys. 4, 42 (2008). 10.1038/nphys788
-
(2008)
Nat. Phys.
, vol.4
, pp. 42
-
-
Larini, L.1
Ottochian, A.2
De Michele, C.3
Leporini, D.4
-
13
-
-
77957759266
-
-
10.1021/ma101649u
-
C. M. Roland, Macromolecules 43, 7875 (2010). 10.1021/ma101649u
-
(2010)
Macromolecules
, vol.43
, pp. 7875
-
-
Roland, C.M.1
-
14
-
-
33746377894
-
Protein misfolding, functional amyloid, and human disease
-
DOI 10.1146/annurev.biochem.75.101304.123901
-
F. Chiti and C. M. Dobson, Annu. Rev. Biochem. 75, 333 (2006). 10.1146/annurev.biochem.75.101304.123901 (Pubitemid 44118036)
-
(2006)
Annual Review of Biochemistry
, vol.75
, pp. 333-366
-
-
Chiti, F.1
Dobson, C.M.2
-
17
-
-
0016610491
-
-
10.1038/253694a0
-
M. Levitt and A. Warshel, Nature 253, 694 (1975). 10.1038/253694a0
-
(1975)
Nature
, vol.253
, pp. 694
-
-
Levitt, M.1
Warshel, A.2
-
18
-
-
0017157584
-
-
10.1016/0022-2836(76)90004-8
-
M. Levitt, J. Mol. Biol. 104, 59 (1976). 10.1016/0022-2836(76)90004-8
-
(1976)
J. Mol. Biol.
, vol.104
, pp. 59
-
-
Levitt, M.1
-
20
-
-
47249101217
-
-
10.1063/1.2943202
-
L. Wu, J. Zhang, M. Qin, F. Liu, and W. Wang, J. Chem. Phys. 128, 235103 (2008). 10.1063/1.2943202
-
(2008)
J. Chem. Phys.
, vol.128
, pp. 235103
-
-
Wu, L.1
Zhang, J.2
Qin, M.3
Liu, F.4
Wang, W.5
-
21
-
-
0242383943
-
Improved Go-like models demonstrate the robustness of protein folding mechanisms towards non-native interactions
-
DOI 10.1016/j.jmb.2003.09.047
-
J. Karanicolas and C. L. Brooks III, J. Mol. Biol. 334, 309 (2003). 10.1016/j.jmb.2003.09.047 (Pubitemid 37357269)
-
(2003)
Journal of Molecular Biology
, vol.334
, Issue.2
, pp. 309-325
-
-
Karanicolas, J.1
Brooks III, C.L.2
-
22
-
-
34547474332
-
The MARTINI force field: Coarse grained model for biomolecular simulations
-
DOI 10.1021/jp071097f
-
S. J. Marrink, H. J. Risselada, S. Yefimov, D. P. Tieleman, and A. H. de Vries, J. Phys. Chem. B 111, 7812 (2007). 10.1021/jp071097f (Pubitemid 47169693)
-
(2007)
Journal of Physical Chemistry B
, vol.111
, Issue.27
, pp. 7812-7824
-
-
Marrink, S.J.1
Risselada, H.J.2
Yefimov, S.3
Tieleman, D.P.4
De Vries, A.H.5
-
23
-
-
23144450194
-
Molecular dynamics with the united-residue model of polypeptide chains. I. Lagrange equations of motion and tests of numerical stability in the microcanonical mode
-
DOI 10.1021/jp058008o
-
M. Khalili, A. Liwo, F. Rakowski, P. Grochowski, and H. A. Scheraga, J. Phys. Chem. B 109, 13785 (2005). 10.1021/jp058008o (Pubitemid 41083971)
-
(2005)
Journal of Physical Chemistry B
, vol.109
, Issue.28
, pp. 13785-13797
-
-
Khalili, M.1
Liwo, A.2
Rakowski, F.3
Grochowski, P.4
Scheraga, H.A.5
-
24
-
-
0004097995
-
-
3rd ed. (Butterworth-Heinemann, Oxford)
-
L. D. Landau, E. M. Lifshitz, E. M. Kosevich, and L. P. Pitaevski, Theory of Elasticity, 3rd ed. (Butterworth-Heinemann, Oxford, 1986).
-
(1986)
Theory of Elasticity
-
-
Landau, L.D.1
Lifshitz, E.M.2
Kosevich, E.M.3
Pitaevski, L.P.4
-
26
-
-
0014709498
-
-
10.1016/S0022-5193(70)80032-7
-
P. Canham, J. Theor. Biol. 26, 61 (1970). 10.1016/S0022-5193(70)80032-7
-
(1970)
J. Theor. Biol.
, vol.26
, pp. 61
-
-
Canham, P.1
-
29
-
-
0037120092
-
-
10.1002/143 9-7641(2002 0916)3:97 54::AID-CPH C7543.0.CO;2-U
-
F. Müller-Plathe, ChemPhysChem 3, 754 (2002). 10.1002/1439- 7641(20020916)3:9754::AID-CPHC7543.0.CO;2-U
-
(2002)
ChemPhysChem
, vol.3
, pp. 754
-
-
Müller-Plathe, F.1
-
30
-
-
46149109506
-
-
10.1063/1.2938860
-
W. G. Noid, J.-W. Chu, G. S. Ayton, V. Krishna, S. Izvekov, G. A. Voth, A. Das, and H. C. Andersen, J. Chem. Phys. 128, 244114 (2008). 10.1063/1.2938860
-
(2008)
J. Chem. Phys.
, vol.128
, pp. 244114
-
-
Noid, W.G.1
Chu, J.-W.2
Ayton, G.S.3
Krishna, V.4
Izvekov, S.5
Voth, G.A.6
Das, A.7
Andersen, H.C.8
-
32
-
-
0036703676
-
Water structure from scattering experiments and simulation
-
DOI 10.1021/cr0006831
-
T. Head-Gordon and G. Hura, Chem. Rev. 102, 2651 (2002). 10.1021/cr0006831 (Pubitemid 35377628)
-
(2002)
Chemical Reviews
, vol.102
, Issue.8
, pp. 2651-2670
-
-
Head-Gordon, T.1
Hura, G.2
-
33
-
-
0027441950
-
Essential dynamics of proteins
-
DOI 10.1002/prot.340170408
-
A. Amadei, A. B. Linssen, and H. J. Berendsen, Proteins 17, 412 (1993). 10.1002/prot.340170408 (Pubitemid 23358549)
-
(1993)
Proteins: Structure, Function and Genetics
, vol.17
, Issue.4
, pp. 412-425
-
-
Amadei, A.1
Linssen, A.B.M.2
Berendsen, H.J.C.3
-
34
-
-
28844466824
-
Slow protein conformational dynamics from multiple experimental structures: The helix/sheet transition of Arc repressor
-
DOI 10.1016/j.str.2005.08.009, PII S0969212605003175
-
R. B. Best, Y. G. Chen, and G. Hummer, Structure 13, 1755 (2005). 10.1016/j.str.2005.08.009 (Pubitemid 41772944)
-
(2005)
Structure
, vol.13
, Issue.12
, pp. 1755-1763
-
-
Best, R.B.1
Chen, Y.-G.2
Hummer, G.3
-
36
-
-
0037847500
-
Colloquium: Geometrical approach to protein folding: A tube picture
-
DOI 10.1103/RevModPhys.75.23
-
J. R. Banavar and A. Maritan, Rev. Mod. Phys. 75, 23 (2003). 10.1103/RevModPhys.75.23 (Pubitemid 36539838)
-
(2003)
Reviews of Modern Physics
, vol.75
, Issue.1
, pp. 23-34
-
-
Banavar, J.R.1
Maritan, A.2
-
37
-
-
4243744350
-
-
10.1016/0375-9601(90)90023-H
-
J. E. I Garrigs, Phys. Lett. A 146, 21 (1990). 10.1016/0375-9601(90) 90023-H
-
(1990)
Phys. Lett. A
, vol.146
, pp. 21
-
-
Garrigs, J.E.I.1
-
39
-
-
34247251976
-
Representability problems for coarse-grained water potentials
-
DOI 10.1063/1.2715953
-
M. E. Johnson, T. Head-Gordon, and A. A. Louis, J. Chem. Phys. 126, 144509 (2007). 10.1063/1.2715953 (Pubitemid 46610010)
-
(2007)
Journal of Chemical Physics
, vol.126
, Issue.14
, pp. 144509
-
-
Johnson, M.E.1
Head-Gordon, T.2
Louis, A.A.3
-
40
-
-
0037078449
-
Beware of density dependent pair potentials
-
DOI 10.1088/0953-8984/14/40/311, PII S0953898402365664, Liquid State Theory, from White Dwarfs to Colloids
-
A. A. Louis, J. Phys.: Condens. Matter 14, 9187 (2002). 10.1088/0953-8984/14/40/311 (Pubitemid 35275047)
-
(2002)
Journal of Physics Condensed Matter
, vol.14
, Issue.40
, pp. 9187-9206
-
-
Louis, A.A.1
-
41
-
-
54949109484
-
-
10.1063/1.2992060
-
M. S. Shell, J. Chem. Phys. 129, 144108 (2008). 10.1063/1.2992060
-
(2008)
J. Chem. Phys.
, vol.129
, pp. 144108
-
-
Shell, M.S.1
-
42
-
-
34248359980
-
Multiscale coarse-graining and structural correlations: Connections to liquid-state theory
-
DOI 10.1021/jp068549t
-
W. G. Noid, J.-W. Chu, G. S. Ayton, and G. A. Voth, J. Phys. Chem. B 111, 4116 (2007). 10.1021/jp068549t (Pubitemid 46732961)
-
(2007)
Journal of Physical Chemistry B
, vol.111
, Issue.16
, pp. 4116-4127
-
-
Noid, W.G.1
Chu, J.-W.2
Ayton, G.S.3
Voth, G.A.4
-
43
-
-
3042598406
-
-
10.1063/1.1739396
-
S. Izvekov, M. Parrinello, C. J. Burnham, and G. A. Voth, J. Chem. Phys. 120, 10896 (2004). 10.1063/1.1739396
-
(2004)
J. Chem. Phys.
, vol.120
, pp. 10896
-
-
Izvekov, S.1
Parrinello, M.2
Burnham, C.J.3
Voth, G.A.4
-
44
-
-
14544291957
-
A multiscale coarse-graining method for biomolecular systems
-
DOI 10.1021/jp044629q
-
S. Izvekov and G. A. Voth, J. Phys. Chem. B 109, 2469 (2005). 10.1021/jp044629q (Pubitemid 40304419)
-
(2005)
Journal of Physical Chemistry B
, vol.109
, Issue.7
, pp. 2469-2473
-
-
Izvekov, S.1
Voth, G.A.2
-
45
-
-
33750181654
-
Modeling real dynamics in the coarse-grained representation of condensed phase systems
-
DOI 10.1063/1.2360580
-
S. Izvekov and G. A. Voth, J. Chem. Phys. 125, 151101 (2006). 10.1063/1.2360580 (Pubitemid 44601772)
-
(2006)
Journal of Chemical Physics
, vol.125
, Issue.15
, pp. 151101
-
-
Izvekov, S.1
Voth, G.A.2
-
46
-
-
33644903231
-
-
10.1021/jp0548220
-
Y. T. Wang, S. Izvekov, T. Y. Yan, and G. A. Voth, J. Phys. Chem. B 110, 3564 (2006). 10.1021/jp0548220
-
(2006)
J. Phys. Chem. B
, vol.110
, pp. 3564
-
-
Wang, Y.T.1
Izvekov, S.2
Yan, T.Y.3
Voth, G.A.4
-
47
-
-
33847717840
-
Smart resolution replica exchange: An efficient algorithm for exploring complex energy landscapes
-
DOI 10.1063/1.2408415
-
P. Liu and G. A. Voth, J. Chem. Phys. 126, 045106 (2007). 10.1063/1.2408415 (Pubitemid 46379139)
-
(2007)
Journal of Chemical Physics
, vol.126
, Issue.4
, pp. 045106
-
-
Liu, P.1
Voth, G.A.2
-
48
-
-
33748266722
-
Mixed atomistic and coarse-grained molecular dynamics: Simulation of a membrane-bound ion channel
-
DOI 10.1021/jp062700h
-
Q. Shi, S. Izvekov, and G. A. Voth, J. Phys. Chem. B 110, 15045 (2006). 10.1021/jp062700h (Pubitemid 44318467)
-
(2006)
Journal of Physical Chemistry B
, vol.110
, Issue.31
, pp. 15045-15048
-
-
Shi, Q.1
Izvekov, S.2
Voth, G.A.3
-
49
-
-
34247098754
-
Multiscale modeling of biomolecular systems: in serial and in parallel
-
DOI 10.1016/j.sbi.2007.03.004, PII S0959440X07000346, Theory and Simulation / Mecromolecular Assemblages
-
G. S. Ayton, W. G. Noid, and G. A. Voth, Curr. Opin. Struct. Biol. 17, 192 (2007). 10.1016/j.sbi.2007.03.004 (Pubitemid 46584804)
-
(2007)
Current Opinion in Structural Biology
, vol.17
, Issue.2
, pp. 192-198
-
-
Ayton, G.S.1
Noid, W.G.2
Voth, G.A.3
-
50
-
-
46149099398
-
-
10.1063/1.2938857
-
W. G. Noid, P. Liu, Y. T. Wang, J.-W. Chu, G. S. Ayton, S. Izvekov, H. C. Andersen, and G. A. Voth, J. Chem. Phys. 128, 244115 (2008). 10.1063/1.2938857
-
(2008)
J. Chem. Phys.
, vol.128
, pp. 244115
-
-
Noid, W.G.1
Liu, P.2
Wang, Y.T.3
Chu, J.-W.4
Ayton, G.S.5
Izvekov, S.6
Andersen, H.C.7
Voth, G.A.8
-
51
-
-
77950149115
-
-
10.1021/ct900643r
-
L. Lu, S. Izvekov, A. Das, H. C. Andersen, and G. A. Voth, J. Chem. Theor. Comp. 6, 954 (2010). 10.1021/ct900643r
-
(2010)
J. Chem. Theor. Comp.
, vol.6
, pp. 954
-
-
Lu, L.1
Izvekov, S.2
Das, A.3
Andersen, H.C.4
Voth, G.A.5
-
52
-
-
73949097591
-
-
10.1021/ct900369w
-
V. Rhle, C. Junghans, A. Lukyanov, K. Kremer, and D. Andrienko, J. Chem. Theor. Comp. 5, 3211 (2009). 10.1021/ct900369w
-
(2009)
J. Chem. Theor. Comp.
, vol.5
, pp. 3211
-
-
Rhle, V.1
Junghans, C.2
Lukyanov, A.3
Kremer, K.4
Andrienko, D.5
-
54
-
-
0004161838
-
-
(Cambridge University Press, New York)
-
W. H. Press, S. A. Teukolsky, W. T. Vetterling, and B. P. Flannery, Numerical Recipes in FORTRAN: The Art of Scientific Computing (Cambridge University Press, New York, 1992).
-
(1992)
Numerical Recipes in FORTRAN: The Art of Scientific Computing
-
-
Press, W.H.1
Teukolsky, S.A.2
Vetterling, W.T.3
Flannery, B.P.4
-
58
-
-
0001317392
-
-
10.1103/PhysRevLett.42.859
-
R. H. Swendsen, Phys. Rev. Lett. 42, 859 (1979). 10.1103/PhysRevLett.42. 859
-
(1979)
Phys. Rev. Lett.
, vol.42
, pp. 859
-
-
Swendsen, R.H.1
-
59
-
-
62349124337
-
-
10.1039/b818051b
-
T. Murtola, A. Bunker, I. Vattulainen, M. Deserno, and M. Karttunen, Phys. Chem. Chem. Phys. 11, 1869 (2009). 10.1039/b818051b
-
(2009)
Phys. Chem. Chem. Phys.
, vol.11
, pp. 1869
-
-
Murtola, T.1
Bunker, A.2
Vattulainen, I.3
Deserno, M.4
Karttunen, M.5
-
61
-
-
68049123310
-
-
10.1016/j.bpj.2009.02.067
-
A. Savelyev and G. A. Papoian, Biophys. J. 96, 4044 (2009). 10.1016/j.bpj.2009.02.067
-
(2009)
Biophys. J.
, vol.96
, pp. 4044
-
-
Savelyev, A.1
Papoian, G.A.2
-
65
-
-
24644483073
-
Large amplitude conformational change in proteins explored with a plastic network model: Adenylate kinase
-
DOI 10.1016/j.jmb.2005.07.031, PII S0022283605008193
-
P. Maragakis and M. Karplus, J. Mol. Biol. 352, 807 (2005). 10.1016/j.jmb.2005.07.031 (Pubitemid 41267070)
-
(2005)
Journal of Molecular Biology
, vol.352
, Issue.4
, pp. 807-822
-
-
Maragakis, P.1
Karplus, M.2
-
66
-
-
0000197372
-
-
10.1103/PhysRevLett.77.1905
-
M. M. Tirion, Phys. Rev. Lett. 77, 1905 (1996). 10.1103/PhysRevLett.77. 1905
-
(1996)
Phys. Rev. Lett.
, vol.77
, pp. 1905
-
-
Tirion, M.M.1
-
69
-
-
10644250257
-
-
10.1103/PhysRev.136.B864
-
P. Hohenberg and W. Kohn, Phys. Rev. 136, B864 (1964). 10.1103/PhysRev.136.B864
-
(1964)
Phys. Rev.
, vol.136
, pp. 864
-
-
Hohenberg, P.1
Kohn, W.2
-
70
-
-
36049046910
-
-
10.1103/PhysRev.137.A1441
-
N. D. Mermin, Phys. Rev. 137, A1441 (1965). 10.1103/PhysRev.137.A1441
-
(1965)
Phys. Rev.
, vol.137
, pp. 1441
-
-
Mermin, N.D.1
-
73
-
-
0002756891
-
-
10.1016/0375-9601(74)90847-0
-
R. L. Henderson, Phys. Lett. A 49, 197 (1974). 10.1016/0375-9601(74) 90847-0
-
(1974)
Phys. Lett. A
, vol.49
, pp. 197
-
-
Henderson, R.L.1
-
76
-
-
84941476533
-
-
10.1515/crll.1909.136.210
-
E. Hellinger, J. Reine Angew. Math. 136, 210 (1909). 10.1515/crll.1909. 136.210
-
(1909)
J. Reine Angew. Math.
, vol.136
, pp. 210
-
-
Hellinger, E.1
-
77
-
-
0000204608
-
-
10.1214/aos/1176343842
-
R. J. Beran, Ann. Stat. 5, 445 (1977). 10.1214/aos/1176343842
-
(1977)
Ann. Stat.
, vol.5
, pp. 445
-
-
Beran, R.J.1
-
79
-
-
70449886281
-
-
10.1103/PhysRevLett.103.198104
-
J. W. Mullinax and W. G. Noid, Phys. Rev. Lett. 103, 198104 (2009). 10.1103/PhysRevLett.103.198104
-
(2009)
Phys. Rev. Lett.
, vol.103
, pp. 198104
-
-
Mullinax, J.W.1
Noid, W.G.2
-
81
-
-
77954232282
-
-
10.1103/PhysRevE.81.060104
-
A. Chaimovich and M. S. Shell, Phys. Rev. E 81, 060104 (2010). 10.1103/PhysRevE.81.060104
-
(2010)
Phys. Rev. e
, vol.81
, pp. 060104
-
-
Chaimovich, A.1
Shell, M.S.2
|