-
1
-
-
84986512474
-
Charmm -A program for macromolecular energy, minimization, and dynamics calculations
-
B.R. Brooks, R.E. Bruccoleri, B.D. Olafson, D.J. States, S. Swaminathan, and M. Karplus, CHARMM -A program for macromolecular energy, minimization, and dynamics calculations, J. Comput. Chem. 4 (1983), pp. 187-217.
-
(1983)
J. Comput. Chem.
, vol.4
, pp. 187-217
-
-
Brooks, B.R.1
Bruccoleri, R.E.2
Olafson, B.D.3
States, D.J.4
Swaminathan, S.5
Karplus, M.6
-
2
-
-
0002062192
-
An empirical potential energy function for phospholipids: Criteriafor parameter optimization and applications
-
K.M. Merz and B. Roux, eds. Birkhauser, Boston, MA
-
M. Schlenkrich, J. Brickmann, A.D. MacKerell, Jr, and M. Karplus, An empirical potential energy function for phospholipids: Criteriafor parameter optimization and applications, in Biological Membranes: A Molecular Perspective from Computation and Experiment, K.M. Merz and B. Roux, eds., Birkhauser, Boston, MA, 1996, pp. 31-81.
-
(1996)
Biological Membranes: A Molecular Perspective from Computation and Experiment
, pp. 31-81
-
-
Schlenkrich, M.1
Brickmann, J.2
MacKerell Jr., A.D.3
Karplus, M.4
-
3
-
-
0034250744
-
An improved empirical potential energy function for molecular simulations of phospholipids
-
S.E. Feller, and A.D. MacKerell, Jr, An improved empirical potential energy function for molecular simulations of phospholipids, J. Phys. Chem. B 104 (2000), pp. 7510-7515.
-
(2000)
J. Phys. Chem. B
, vol.104
, pp. 7510-7515
-
-
Feller, S.E.1
MacKerell Jr., A.D.2
-
4
-
-
15744368593
-
An ab initio study on the torsional surface of alkanes and its effect on molecular simulations of alkanes and a dppc bilayer
-
J.B. Klauda, B.R. Brooks, A.D. MacKerell, Jr., R.M. Venable, and R.W. Pastor, An ab initio study on the torsional surface of alkanes and its effect on molecular simulations of alkanes and a DPPC bilayer, J. Phys. Chem. B 109 (2005), pp. 5300-5311.
-
(2005)
J. Phys. Chem. B
, vol.109
, pp. 5300-5311
-
-
Klauda, J.B.1
Brooks, B.R.2
MacKerell Jr., A.D.3
Venable, R.M.4
Pastor, R.W.5
-
6
-
-
0030999097
-
Molecular dynamics simulations of a fluid bilayer of dipalmitoylphosphatidylcholine at full hydration, constant pressure, and constant temperature
-
O. Berger, O. Edholm, and F. Jähnig, Molecular dynamics simulations of a fluid bilayer of dipalmitoylphosphatidylcholine at full hydration, constant pressure, and constant temperature, Biophys. J. 72 (1997), pp. 2002-2013.
-
(1997)
Biophys. J.
, vol.72
, pp. 2002-2013
-
-
Berger, O.1
Edholm, O.2
Jähnig, F.3
-
7
-
-
0035425883
-
An improved gromos96 force field for aliphatic hydrocarbons in the condensed phase
-
L.D. Schuler, X. Daura, and W.F. van Gunsteren, An improved GROMOS96 force field for aliphatic hydrocarbons in the condensed phase, J. Comput. Chem. 22 (2001), pp. 1205-1218.
-
(2001)
J. Comput. Chem.
, vol.22
, pp. 1205-1218
-
-
Schuler, L.D.1
Daura, X.2
Van Gunsteren, W.F.3
-
8
-
-
4444282928
-
A biomolecular force field based on the free enthalpy of hydration and solvation: The gromos force-field parameter sets 53a5 and 53a6
-
C. Oostenbrink, A. Villa, A.E. Mark, and W.F. van Gunsteren, A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force-field parameter sets 53A5 and 53A6, J. Comput. Chem. 25 (2004), pp. 1656-1676.
-
(2004)
J. Comput. Chem.
, vol.25
, pp. 1656-1676
-
-
Oostenbrink, C.1
Villa, A.2
Mark, A.E.3
Van Gunsteren, W.F.4
-
9
-
-
34250372191
-
Reparameterization of all-Atom dipalmitoylphosphatidylcholine lipid parameters enables simulation of fluid bilayers at zero tension
-
J. Sonne, M.O. Jensen, F.Y. Hansen, L. Hemmingsen, and G.H. Peters, Reparameterization of all-Atom dipalmitoylphosphatidylcholine lipid parameters enables simulation of fluid bilayers at zero tension, Biophys. J. 92 (2007), pp. 4157-4167.
-
(2007)
Biophys. J.
, vol.92
, pp. 4157-4167
-
-
Sonne, J.1
Jensen, M.O.2
Hansen, F.Y.3
Hemmingsen, L.4
Peters, G.H.5
-
10
-
-
52649147983
-
Modification of the charmm force field for dmpc lipid bilayer
-
G.J. Högberg, A.M. Nikitin, and A.P. Lyubartsev, Modification of the CHARMM force field for DMPC lipid bilayer, J. Comp. Chem. 29 (2008), pp. 2359-2369.
-
(2008)
J. Comp. Chem.
, vol.29
, pp. 2359-2369
-
-
Högberg, G.J.1
Nikitin, A.M.2
Lyubartsev, A.P.3
-
11
-
-
60649103257
-
Validation of all-Atom phosphatidylcholine lipid force fields in the tensionless npt ensemble
-
J. Taylor, N.E. Whiteford, G. Bradley, and G.W. Watson, Validation of all-Atom phosphatidylcholine lipid force fields in the tensionless NPT ensemble, Biochim. Biophys. Acta 1788 (2009), pp. 638-649.
-
(2009)
Biochim. Biophys. Acta
, vol.1788
, pp. 638-649
-
-
Taylor, J.1
Whiteford, N.E.2
Bradley, G.3
Watson, G.W.4
-
12
-
-
33744920795
-
Closer look at structure of fully hydrated fluid phase dppc bilayers
-
N. Kučerka, S.T. Nagle, and J.F. Nagle, Closer look at structure of fully hydrated fluid phase DPPC bilayers, Biophys. J.: Biophys. Lett. 90 (2006), p. L83.
-
(2006)
Biophys. J.: Biophys. Lett.
, vol.90
-
-
Kučerka, N.1
Nagle, S.T.2
Nagle, J.F.3
-
13
-
-
77953377650
-
Update of the charmm all-Atom additive force field for lipids: Validation on six lipid types
-
J.B. Klauda, R.M. Venable, J.A. Freites, J.W. O'Connor, D.J. Tobias, C. Mondragon-Ramirez, I. Vorobyov, A.D. MacKerell, Jr, and R.W. Pastor, Update of the CHARMM all-Atom additive force field for lipids: Validation on six lipid types, J. Phys. Chem. B 114 (2010), pp. 7830-7843.
-
(2010)
J. Phys. Chem. B
, vol.114
, pp. 7830-7843
-
-
Klauda, J.B.1
Venable, R.M.2
Freites, J.A.3
O'Connor, J.W.4
Tobias, D.J.5
Mondragon-Ramirez, C.6
Vorobyov, I.7
MacKerell Jr., A.D.8
Pastor, R.W.9
-
14
-
-
0030033065
-
X-ray structure determination of fully hydrated la phase dipalmitoylphosphatidylcholine bilayers
-
J.F. Nagle, R. Zhang, S. Tristram-Nagle, W. Sun, H.I. Petrache, and R.M. Suter, X-ray structure determination of fully hydrated La phase dipalmitoylphosphatidylcholine bilayers, Biophys. J. 70 (1996), pp. 1419-1431.
-
(1996)
Biophys. J.
, vol.70
, pp. 1419-1431
-
-
Nagle, J.F.1
Zhang, R.2
Tristram-Nagle, S.3
Sun, W.4
Petrache, H.I.5
Suter, R.M.6
-
15
-
-
33646446451
-
Structure of fully hydrated phase lipid bilayers with monounsaturated chains
-
N. Kučerka, S. Tristram-Nagle, and J.F. Nagle, Structure of fully hydrated phase lipid bilayers with monounsaturated chains, J. Membrane Biol. 208 (2005), pp. 193-202.
-
(2005)
J. Membrane Biol.
, vol.208
, pp. 193-202
-
-
Kučerka, N.1
Tristram-Nagle, S.2
Nagle, J.F.3
-
16
-
-
33751157933
-
Solvent induced forces between two hydrophilic groups
-
S.R. Durell, B.R. Brooks, and A. Ben-Naim, Solvent induced forces between two hydrophilic groups, J. Phys. Chem. 98 (1994), pp. 2198-2202.
-
(1994)
J. Phys. Chem.
, vol.98
, pp. 2198-2202
-
-
Durell, S.R.1
Brooks, B.R.2
Ben-Naim, A.3
-
17
-
-
33846823909
-
Particle mesh ewald: An nlog(n) method for ewald sums in large systems
-
T. Darden, D. York, and L. Pederesn, Particle mesh Ewald: An Nlog(n) method for Ewald sums in large systems, J. Chem. Phys. 98 (1993), pp. 10089-10093.
-
(1993)
J. Chem. Phys.
, vol.98
, pp. 10089-10093
-
-
Darden, T.1
York, D.2
Pederesn, L.3
-
18
-
-
26144434487
-
Crystal structure and pair potentials: A molecular dynamics study
-
M. Parrinello and A. Rahman, Crystal structure and pair potentials: A molecular dynamics study, Phys. Rev. Lett. 45 (1980), pp. 1196-1199.
-
(1980)
Phys. Rev. Lett.
, vol.45
, pp. 1196-1199
-
-
Parrinello, M.1
Rahman, A.2
-
19
-
-
34547809547
-
A unified formulation of the constant temperature molecular dynamics methods
-
S. Nosé, A unified formulation of the constant temperature molecular dynamics methods, J. Chem. Phys. 81 (1984), pp. 511-520.
-
(1984)
J. Chem. Phys.
, vol.81
, pp. 511-520
-
-
Nosé, S.1
-
20
-
-
36449000062
-
Nosé -hoover chains: The canonical ensemble via continuous dynamics
-
G.J. Martyna, M.E. Tuckerman, and M.L. Klein, Nosé -Hoover chains: The canonical ensemble via continuous dynamics, J. Chem. Phys. 97 (1992), pp. 2635-2644.
-
(1992)
J. Chem. Phys.
, vol.97
, pp. 2635-2644
-
-
Martyna, G.J.1
Tuckerman, M.E.2
Klein, M.L.3
-
21
-
-
0000026966
-
Explicit reversible integrators for extended systems dynamics
-
G.J. Martyna, M.E. Tuckerman, D.J. Tobias, and M.L. Klein, Explicit reversible integrators for extended systems dynamics, Mol. Phys. 87 (1996), pp. 1117-1157.
-
(1996)
Mol. Phys.
, vol.87
, pp. 1117-1157
-
-
Martyna, G.J.1
Tuckerman, M.E.2
Tobias, D.J.3
Klein, M.L.4
-
23
-
-
0035857205
-
Effect of unsaturated lipid chains on dimensions, molecular order and hydration of membranes, j
-
H. Binder and K. Gawrisch, Effect of unsaturated lipid chains on dimensions, molecular order and hydration of membranes, J. Phys. Chem. B 105 (2001), pp. 12378-12390.
-
(2001)
Phys. Chem. B
, vol.105
, pp. 12378-12390
-
-
Binder, H.1
Gawrisch, K.2
-
24
-
-
84882884096
-
High pressure effects in molecular bioscience
-
M.R. Manna, ed. Elsevier Amsterdam
-
R. Winter, High pressure effects in molecular bioscience, in Chemistry at Extreme Conditions, M.R. Manna, ed., Elsevier, Amsterdam, 2004, pp. 29-82.
-
(2004)
Chemistry at Extreme Conditions
, pp. 29-82
-
-
Winter, R.1
-
25
-
-
0032504528
-
Compressibility and density of lipid bilayers composed of polyunsaturated phospholipids and cholesterol
-
T. Hianik, M. Haburcák, K. Lohner, E. Prenner, F. Paaltauf, and A. Hermetter, Compressibility and density of lipid bilayers composed of polyunsaturated phospholipids and cholesterol, Colloid Surf. A: Physicochem. Eng. Aspects 139 (1998), pp. 189-197.
-
(1998)
Colloid Surf. A: Physicochem. Eng. Aspects
, vol.139
, pp. 189-197
-
-
Hianik, T.1
Haburcák, M.2
Lohner, K.3
Prenner, E.4
Paaltauf, F.5
Hermetter, A.6
-
26
-
-
0016283654
-
Phospholipid bilayer measured by deuterium magnetic resonance
-
A. Seelig and J. Seelig, Phospholipid bilayer measured by deuterium magnetic resonance, Biochemistry 13 (1974), pp. 4839-4845.
-
(1974)
Biochemistry
, vol.13
, pp. 4839-4845
-
-
Seelig, A.1
Seelig, J.2
-
27
-
-
0028929692
-
Restatement of order parameters in biomembranes: Calculation of czc bond order parameters from c-d quadrupolar splittings
-
J.P. Douliez, A. Léonard, and E.J. Dufourc, Restatement of order parameters in biomembranes: Calculation of CZC bond order parameters from C-D quadrupolar splittings, Biophys. J. 68 (1995), pp. 1727-1739.
-
(1995)
Biophys. J.
, vol.68
, pp. 1727-1739
-
-
Douliez, J.P.1
Léonard, A.2
Dufourc, E.J.3
-
28
-
-
0017808625
-
Molecular order in cis and trans unsaturated phospholipid bilayers
-
J. Seelig and N. Waespe-Sǎrčevic, Molecular order in cis and trans unsaturated phospholipid bilayers, Biochemistry 17 (1978), pp. 3310-3315.
-
(1978)
Biochemistry
, vol.17
, pp. 3310-3315
-
-
Seelig, J.1
Waespe-Sǎrčevic, N.2
|