-
1
-
-
0003505783
-
-
2nd ed. Academic Press, Inc. San Diego, CA
-
Yeagle, P. L. The membranes of cells; 2nd ed.; Academic Press, Inc.: San Diego, CA, 1993.
-
(1993)
The Membranes of Cells
-
-
Yeagle, P.L.1
-
2
-
-
0001143770
-
Orientation and diffusion of a drug analog in biomembranes: Molecular dynamics simulations
-
Alper, H. E.; Stouch, T. R. Orientation and diffusion of a drug analog in biomembranes: molecular dynamics simulations J. Phys. Chem. 1995, 99, 5724-5731
-
(1995)
J. Phys. Chem.
, vol.99
, pp. 5724-5731
-
-
Alper, H.E.1
Stouch, T.R.2
-
3
-
-
0000454817
-
Mechanism of solute diffusion through lipid bilayer membranes by molecular dynamics simulation
-
Bassolino-Klimas, D.; Alper, H. E.; Stouch, T. R. Mechanism of solute diffusion through lipid bilayer membranes by molecular dynamics simulation J. Am. Chem. Soc. 1995, 117, 4118-4129
-
(1995)
J. Am. Chem. Soc.
, vol.117
, pp. 4118-4129
-
-
Bassolino-Klimas, D.1
Alper, H.E.2
Stouch, T.R.3
-
4
-
-
0031755264
-
Effects of anesthetics on the structure of a phospholipid bilayer: Molecular dynamics investigation of halothane in the hydrated liquid crystal phase of dipalmitoylphosphatidylcholine
-
Tu, K.; Tarek, M.; Klein, M. L.; Scharf, D. Effects of anesthetics on the structure of a phospholipid bilayer: molecular dynamics investigation of halothane in the hydrated liquid crystal phase of dipalmitoylphosphatidylcholine Biophys. J. 1998, 75, 2123-2134
-
(1998)
Biophys. J.
, vol.75
, pp. 2123-2134
-
-
Tu, K.1
Tarek, M.2
Klein, M.L.3
Scharf, D.4
-
5
-
-
10644227774
-
Molecular-level organization of saturated and polyunsaturated fatty acids in a phosphatidylcholine bilayer containing cholesterol
-
Pitman, M. C.; Suits, F.; MacKerell, A. D., Jr.; Feller, S. E. Molecular-level organization of saturated and polyunsaturated fatty acids in a phosphatidylcholine bilayer containing cholesterol Biochemistry 2004, 43, 15318-15328
-
(2004)
Biochemistry
, vol.43
, pp. 15318-15328
-
-
Pitman, M.C.1
Suits, F.2
MacKerell, Jr.A.D.3
Feller, S.E.4
-
6
-
-
0346057941
-
Distribution of pentachlorophenol in phospholipid bilayers: A molecular dynamics study
-
Mukhopadhyay, P.; Vogel, H. J.; Tieleman, D. P. Distribution of pentachlorophenol in phospholipid bilayers: a molecular dynamics study Biophys. J. 2004, 86, 337-345
-
(2004)
Biophys. J.
, vol.86
, pp. 337-345
-
-
Mukhopadhyay, P.1
Vogel, H.J.2
Tieleman, D.P.3
-
7
-
-
28144454423
-
Behaviour of small solutes and large drugs in a lipid bilayer from computer simulations
-
Bemporad, D.; Luttmann, C.; Essex, J. W. Behaviour of small solutes and large drugs in a lipid bilayer from computer simulations Biochim. Biophys. Acta, Biomembr. 2005, 1718, 1-21
-
(2005)
Biochim. Biophys. Acta, Biomembr.
, vol.1718
, pp. 1-21
-
-
Bemporad, D.1
Luttmann, C.2
Essex, J.W.3
-
8
-
-
33748493587
-
Indole localization in lipid membranes revealed by molecular simulation
-
Norman, K. E.; Nymeyer, H. Indole localization in lipid membranes revealed by molecular simulation Biophys. J. 2006, 91, 2046-2054
-
(2006)
Biophys. J.
, vol.91
, pp. 2046-2054
-
-
Norman, K.E.1
Nymeyer, H.2
-
9
-
-
33751158845
-
Simulation of water transport through a lipid membrane
-
Marrink, S.-J.; Berendsen, H. J. C. Simulation of water transport through a lipid membrane J. Phys. Chem. 1994, 98, 4155-4168
-
(1994)
J. Phys. Chem.
, vol.98
, pp. 4155-4168
-
-
Marrink, S.-J.1
Berendsen, H.J.C.2
-
10
-
-
3142721955
-
Molecular dynamics study on the effects of chain branching on the physical properties of lipid bilayers. 2. Permeability
-
Shinoda, W.; Mikami, M.; Baba, T.; Hato, M. Molecular dynamics study on the effects of chain branching on the physical properties of lipid bilayers. 2. Permeability J. Phys. Chem. B 2004, 108, 9346-9356
-
(2004)
J. Phys. Chem. B
, vol.108
, pp. 9346-9356
-
-
Shinoda, W.1
Mikami, M.2
Baba, T.3
Hato, M.4
-
11
-
-
73949096788
-
Simulated tempering distributed replica sampling, virtual replica exchange, and other generalized-ensemble methods for conformational sampling
-
Rauscher, S.; Neale, C.; Pomès, R. Simulated tempering distributed replica sampling, virtual replica exchange, and other generalized-ensemble methods for conformational sampling J. Chem. Theory Comput. 2009, 5, 2640-2662
-
(2009)
J. Chem. Theory Comput.
, vol.5
, pp. 2640-2662
-
-
Rauscher, S.1
Neale, C.2
Pomès, R.3
-
12
-
-
33847361456
-
Convergence of molecular dynamics simulations of membrane proteins
-
Grossfield, A.; Feller, S. E.; Pitman, M. C. Convergence of molecular dynamics simulations of membrane proteins Proteins 2007, 67, 31-40
-
(2007)
Proteins
, vol.67
, pp. 31-40
-
-
Grossfield, A.1
Feller, S.E.2
Pitman, M.C.3
-
13
-
-
83455177932
-
Statistical convergence of equilibrium properties in simulations of molecular solutes embedded in lipid bilayers
-
Neale, C.; Bennett, W. F. D.; Tieleman, D. P.; Pomès, R. Statistical convergence of equilibrium properties in simulations of molecular solutes embedded in lipid bilayers J. Chem. Theory Comput. 2011, 7, 4175-4188
-
(2011)
J. Chem. Theory Comput.
, vol.7
, pp. 4175-4188
-
-
Neale, C.1
Bennett, W.F.D.2
Tieleman, D.P.3
Pomès, R.4
-
14
-
-
79955874370
-
Equilibrium sampling in biomolecular simulations
-
Zuckerman, D. M. Equilibrium sampling in biomolecular simulations Annu. Rev. Biophys. 2011, 40, 41-62
-
(2011)
Annu. Rev. Biophys.
, vol.40
, pp. 41-62
-
-
Zuckerman, D.M.1
-
15
-
-
41949112774
-
Molecular simulation as an aid to experimentalists
-
van Gunsteren, W. F.; Dolenc, J.; Mark, A. E. Molecular simulation as an aid to experimentalists Curr. Opin. Struct. Biol. 2008, 18, 149-153
-
(2008)
Curr. Opin. Struct. Biol.
, vol.18
, pp. 149-153
-
-
Van Gunsteren, W.F.1
Dolenc, J.2
Mark, A.E.3
-
16
-
-
33646943202
-
Molecular dynamics: Survey of methods for simulating the activity of proteins
-
Adcock, S. A.; McCammon, J. A. Molecular dynamics: survey of methods for simulating the activity of proteins Chem. Rev. 2006, 106, 1589-1615
-
(2006)
Chem. Rev.
, vol.106
, pp. 1589-1615
-
-
Adcock, S.A.1
McCammon, J.A.2
-
17
-
-
0342929614
-
Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling
-
Torrie, G. M.; Valleau, J. P. Nonphysical sampling distributions in Monte Carlo free-energy estimation: umbrella sampling J. Comput. Phys. 1977, 23, 187-199
-
(1977)
J. Comput. Phys.
, vol.23
, pp. 187-199
-
-
Torrie, G.M.1
Valleau, J.P.2
-
18
-
-
0029633155
-
The calculation of the potential of mean force using computer simulations
-
Roux, B. The calculation of the potential of mean force using computer simulations Comput. Phys. Commun. 1995, 91, 275-282
-
(1995)
Comput. Phys. Commun.
, vol.91
, pp. 275-282
-
-
Roux, B.1
-
19
-
-
67849105001
-
Free energy for the permeation of Na+ and Cl- ions and their ion-pair through a zwitterionic dimyristoyl phosphatidylcholine lipid bilayer by umbrella integration with harmonic fourier beads
-
Khavrutskii, I. V.; Gorfe, A. A.; Lu, B.; McCammon, J. A. Free energy for the permeation of Na+ and Cl- ions and their ion-pair through a zwitterionic dimyristoyl phosphatidylcholine lipid bilayer by umbrella integration with harmonic fourier beads J. Am. Chem. Soc. 2009, 131, 1706-1716
-
(2009)
J. Am. Chem. Soc.
, vol.131
, pp. 1706-1716
-
-
Khavrutskii, I.V.1
Gorfe, A.A.2
Lu, B.3
McCammon, J.A.4
-
20
-
-
45849118699
-
Chapter 8 Interactions between small molecules and lipid bilayers
-
In; Scott, E. F. Academic Press: New York
-
MacCallum, J. L.; Tieleman, D. P. Chapter 8 Interactions between small molecules and lipid bilayers. In Curr. Top. Membr.; Scott, E. F., Ed.; Academic Press: New York, 2008; Vol. 60, pp 227-256.
-
(2008)
Curr. Top. Membr.
, vol.60
, pp. 227-256
-
-
MacCallum, J.L.1
Tieleman, D.P.2
-
21
-
-
33751302622
-
Mechanisms of passive ion permeation through lipid bilayers: Insights from simulations
-
Tepper, H. L.; Voth, G. A. Mechanisms of passive ion permeation through lipid bilayers: insights from simulations J. Phys. Chem. B 2006, 110, 21327-21337
-
(2006)
J. Phys. Chem. B
, vol.110
, pp. 21327-21337
-
-
Tepper, H.L.1
Voth, G.A.2
-
22
-
-
17844401731
-
Protons may leak through pure lipid bilayers via a concerted mechanism
-
Tepper, H. L.; Voth, G. A. Protons may leak through pure lipid bilayers via a concerted mechanism Biophys. J. 2005, 88, 3095-3108
-
(2005)
Biophys. J.
, vol.88
, pp. 3095-3108
-
-
Tepper, H.L.1
Voth, G.A.2
-
23
-
-
0029972071
-
Mechanism of unassisted ion transport across membrane bilayers
-
Wilson, M. A.; Pohorille, A. Mechanism of unassisted ion transport across membrane bilayers J. Am. Chem. Soc. 1996, 118, 6580-6587
-
(1996)
J. Am. Chem. Soc.
, vol.118
, pp. 6580-6587
-
-
Wilson, M.A.1
Pohorille, A.2
-
24
-
-
0031175513
-
Interaction of K+ with a phospholipid bilayer: A molecular dynamics study
-
Gambu, I.; Roux, B. Interaction of K+ with a phospholipid bilayer: a molecular dynamics study J. Phys. Chem. B 1997, 101, 6066-6072
-
(1997)
J. Phys. Chem. B
, vol.101
, pp. 6066-6072
-
-
Gambu, I.1
Roux, B.2
-
25
-
-
0037028611
-
Molecular dynamics study of water pores in a phospholipid bilayer
-
Zahn, D.; Brickmann, J. Molecular dynamics study of water pores in a phospholipid bilayer Chem. Phys. Lett. 2002, 352, 441-446
-
(2002)
Chem. Phys. Lett.
, vol.352
, pp. 441-446
-
-
Zahn, D.1
Brickmann, J.2
-
26
-
-
84874903645
-
Implicit inclusion of atomic polarization in modeling of partitioning between water and lipid bilayers
-
Jambeck, J. P. M.; Lyubartsev, A. P. Implicit inclusion of atomic polarization in modeling of partitioning between water and lipid bilayers Phys. Chem. Chem. Phys. 2013, 15, 4677-4686
-
(2013)
Phys. Chem. Chem. Phys.
, vol.15
, pp. 4677-4686
-
-
Jambeck, J.P.M.1
Lyubartsev, A.P.2
-
27
-
-
84858636088
-
Large influence of cholesterol on solute partitioning into lipid membranes
-
Wennberg, C. L.; van der Spoel, D.; Hub, J. S. Large influence of cholesterol on solute partitioning into lipid membranes J. Am. Chem. Soc. 2012, 134, 5351-5361
-
(2012)
J. Am. Chem. Soc.
, vol.134
, pp. 5351-5361
-
-
Wennberg, C.L.1
Van Der Spoel, D.2
Hub, J.S.3
-
28
-
-
30744448428
-
Computer simulation of the distribution of hexane in a lipid bilayer: Spatially resolved free energy, entropy, and enthalpy profiles
-
MacCallum, J. L.; Tieleman, D. P. Computer simulation of the distribution of hexane in a lipid bilayer: spatially resolved free energy, entropy, and enthalpy profiles J. Am. Chem. Soc. 2006, 128, 125-130
-
(2006)
J. Am. Chem. Soc.
, vol.128
, pp. 125-130
-
-
MacCallum, J.L.1
Tieleman, D.P.2
-
29
-
-
0030264744
-
Permeation process of small molecules across lipid membranes studied by molecular dynamics simulations
-
Marrink, S.-J.; Berendsen, H. J. C. Permeation process of small molecules across lipid membranes studied by molecular dynamics simulations J. Phys. Chem. 1996, 100, 16729-16738
-
(1996)
J. Phys. Chem.
, vol.100
, pp. 16729-16738
-
-
Marrink, S.-J.1
Berendsen, H.J.C.2
-
30
-
-
84857080087
-
The role of atomic polarization in the thermodynamics of chloroform partitioning to lipid bilayers
-
Vorobyov, I.; Bennett, W. F. D.; Tieleman, D. P.; Allen, T. W.; Noskov, S. The role of atomic polarization in the thermodynamics of chloroform partitioning to lipid bilayers J. Chem. Theory Comput. 2012, 8, 618-628
-
(2012)
J. Chem. Theory Comput.
, vol.8
, pp. 618-628
-
-
Vorobyov, I.1
Bennett, W.F.D.2
Tieleman, D.P.3
Allen, T.W.4
Noskov, S.5
-
31
-
-
84860542379
-
Diffusion of 1,2-dimethoxyethane and 1,2-dimethoxypropane through phosphatidycholine bilayers: A molecular dynamics study
-
Samanta, S.; Hezaveh, S.; Milano, G.; Roccatano, D. Diffusion of 1,2-dimethoxyethane and 1,2-dimethoxypropane through phosphatidycholine bilayers: a molecular dynamics study J. Phys. Chem. B 2012, 116, 5141-5151
-
(2012)
J. Phys. Chem. B
, vol.116
, pp. 5141-5151
-
-
Samanta, S.1
Hezaveh, S.2
Milano, G.3
Roccatano, D.4
-
32
-
-
0030112112
-
Interactions of anesthetics with the membrane-water interface
-
Pohorille, A.; Cieplak, P.; Wilson, M. A. Interactions of anesthetics with the membrane-water interface Chem. Phys. 1996, 204, 337-345
-
(1996)
Chem. Phys.
, vol.204
, pp. 337-345
-
-
Pohorille, A.1
Cieplak, P.2
Wilson, M.A.3
-
33
-
-
27644522257
-
Interactions of liquid crystal-forming molecules with phospholipid bilayers studied by molecular dynamics simulations
-
Kim, E. B.; Lockwood, N.; Chopra, M.; Guzmán, O.; Abbott, N. L.; de Pablo, J. J. Interactions of liquid crystal-forming molecules with phospholipid bilayers studied by molecular dynamics simulations Biophys. J. 2005, 89, 3141-3158
-
(2005)
Biophys. J.
, vol.89
, pp. 3141-3158
-
-
Kim, E.B.1
Lockwood, N.2
Chopra, M.3
Guzmán, O.4
Abbott, N.L.5
De Pablo, J.J.6
-
34
-
-
84873386975
-
Taste of sugar at the membrane: Thermodynamics and kinetics of the interaction of a disaccharide with lipid bilayers
-
Tian, J.; Sethi, A.; Swanson, B. I.; Goldstein, B.; Gnanakaran, S. Taste of sugar at the membrane: thermodynamics and kinetics of the interaction of a disaccharide with lipid bilayers Biophys. J. 2013, 104, 622-632
-
(2013)
Biophys. J.
, vol.104
, pp. 622-632
-
-
Tian, J.1
Sethi, A.2
Swanson, B.I.3
Goldstein, B.4
Gnanakaran, S.5
-
35
-
-
33749182054
-
Lipids out of equilibrium: Energetics of desorption and pore mediated flip-flop
-
Tieleman, D. P.; Marrink, S.-J. Lipids out of equilibrium: energetics of desorption and pore mediated flip-flop J. Am. Chem. Soc. 2006, 128, 12462-12467
-
(2006)
J. Am. Chem. Soc.
, vol.128
, pp. 12462-12467
-
-
Tieleman, D.P.1
Marrink, S.-J.2
-
36
-
-
70449331690
-
Density imbalances and free energy of lipid transfer in supported lipid bilayers
-
Xing, C.; Faller, R. Density imbalances and free energy of lipid transfer in supported lipid bilayers J. Chem. Phys. 2009, 131, 175104
-
(2009)
J. Chem. Phys.
, vol.131
, pp. 175104
-
-
Xing, C.1
Faller, R.2
-
37
-
-
69349095310
-
Thermodynamics of flip-flop and desorption for a systematic series of phosphatidylcholine lipids
-
Sapay, N.; Bennett, W. F. D.; Tieleman, D. P. Thermodynamics of flip-flop and desorption for a systematic series of phosphatidylcholine lipids Soft Matter 2009, 5, 3295-3302
-
(2009)
Soft Matter
, vol.5
, pp. 3295-3302
-
-
Sapay, N.1
Bennett, W.F.D.2
Tieleman, D.P.3
-
38
-
-
67749129321
-
Thermodynamic analysis of the effect of cholesterol on dipalmitoylphosphatidylcholine lipid membranes
-
Bennett, W. F. D.; MacCallum, J. L.; Tieleman, D. P. Thermodynamic analysis of the effect of cholesterol on dipalmitoylphosphatidylcholine lipid membranes J. Am. Chem. Soc. 2009, 131, 1972-1978
-
(2009)
J. Am. Chem. Soc.
, vol.131
, pp. 1972-1978
-
-
Bennett, W.F.D.1
MacCallum, J.L.2
Tieleman, D.P.3
-
39
-
-
84857748574
-
Molecular simulation of rapid translocation of cholesterol, diacylglycerol, and ceramide in model raft and nonraft membranes
-
Bennett, W. F. D.; Tieleman, D. P. Molecular simulation of rapid translocation of cholesterol, diacylglycerol, and ceramide in model raft and nonraft membranes J. Lipid Res. 2012, 53, 421-429
-
(2012)
J. Lipid Res.
, vol.53
, pp. 421-429
-
-
Bennett, W.F.D.1
Tieleman, D.P.2
-
40
-
-
34548205826
-
The distribution and conformation of very long-chain plant wax components in a lipid bilayer
-
Coll, E. P.; Kandt, C.; Bird, D. A.; Samuels, A. L.; Tieleman, D. P. The distribution and conformation of very long-chain plant wax components in a lipid bilayer J. Phys. Chem. B 2007, 111, 8702-8704
-
(2007)
J. Phys. Chem. B
, vol.111
, pp. 8702-8704
-
-
Coll, E.P.1
Kandt, C.2
Bird, D.A.3
Samuels, A.L.4
Tieleman, D.P.5
-
41
-
-
84877045048
-
Lipid bilayer membrane affinity rationalizes inhibition of lipid peroxidation by a natural lignan antioxidant
-
Podloucká, P.; Berka, K.; Fabre, G.; Paloncýová, M.; Duroux, J.-L.; Otyepka, M.; Trouillas, P. Lipid bilayer membrane affinity rationalizes inhibition of lipid peroxidation by a natural lignan antioxidant. J. Phys. Chem. B 2013, 117, 5043-5049.
-
(2013)
J. Phys. Chem. B
, vol.117
, pp. 5043-5049
-
-
Podloucká, P.1
Berka, K.2
Fabre, G.3
Paloncýová, M.4
Duroux, J.-L.5
Otyepka, M.6
Trouillas, P.7
-
42
-
-
43049156443
-
Energetics of cholesterol transfer between lipid bilayers
-
Zhang, Z.; Lu, L.; Berkowitz, M. L. Energetics of cholesterol transfer between lipid bilayers J. Phys. Chem. B 2008, 112, 3807-3811
-
(2008)
J. Phys. Chem. B
, vol.112
, pp. 3807-3811
-
-
Zhang, Z.1
Lu, L.2
Berkowitz, M.L.3
-
43
-
-
77958498212
-
Cholesterol flip-flop: Insights from free energy simulation studies
-
Jo, S.; Rui, H.; Lim, J. B.; Klauda, J. B.; Im, W. Cholesterol flip-flop: insights from free energy simulation studies J. Phys. Chem. B 2010, 114, 13342-13348
-
(2010)
J. Phys. Chem. B
, vol.114
, pp. 13342-13348
-
-
Jo, S.1
Rui, H.2
Lim, J.B.3
Klauda, J.B.4
Im, W.5
-
44
-
-
69349085157
-
Molecular view of cholesterol flip-flop and chemical potential in different membrane environments
-
Bennett, W. F. D.; MacCallum, J. L.; Hinner, M. J.; Marrink, S.-J.; Tieleman, D. P. Molecular view of cholesterol flip-flop and chemical potential in different membrane environments J. Am. Chem. Soc. 2009, 131, 12714-12720
-
(2009)
J. Am. Chem. Soc.
, vol.131
, pp. 12714-12720
-
-
Bennett, W.F.D.1
MacCallum, J.L.2
Hinner, M.J.3
Marrink, S.-J.4
Tieleman, D.P.5
-
45
-
-
55949124264
-
A steroid in a lipid bilayer: Localization, orientation, and energetics
-
Vijayan, R.; Biggin, P. C. A steroid in a lipid bilayer: localization, orientation, and energetics Biophys. J. 2008, 95, L45-L47
-
(2008)
Biophys. J.
, vol.95
-
-
Vijayan, R.1
Biggin, P.C.2
-
46
-
-
0344119514
-
Permeation across hydrated DPPC lipid bilayers: Simulation of the titrable amphiphilic drug valproic acid
-
Ulander, J.; Haymet, A. D. J. Permeation across hydrated DPPC lipid bilayers: simulation of the titrable amphiphilic drug valproic acid Biophys. J. 2003, 85, 3475-3484
-
(2003)
Biophys. J.
, vol.85
, pp. 3475-3484
-
-
Ulander, J.1
Haymet, A.D.J.2
-
47
-
-
84874625062
-
Molecular insight into affinities of drugs and their metabolites to lipid bilayers
-
Paloncýová, M.; Berka, K.; Otyepka, M. Molecular insight into affinities of drugs and their metabolites to lipid bilayers J. Phys. Chem. B 2013, 117, 2403-2410
-
(2013)
J. Phys. Chem. B
, vol.117
, pp. 2403-2410
-
-
Paloncýová, M.1
Berka, K.2
Otyepka, M.3
-
48
-
-
58749107531
-
Distribution and dynamics of adamantanes in a lipid bilayer
-
Chew, C. F.; Guy, A.; Biggin, P. C. Distribution and dynamics of adamantanes in a lipid bilayer Biophys. J. 2008, 95, 5627-5636
-
(2008)
Biophys. J.
, vol.95
, pp. 5627-5636
-
-
Chew, C.F.1
Guy, A.2
Biggin, P.C.3
-
49
-
-
77249136326
-
Partitioning of nonsteroidal antiinflammatory drugs in lipid membranes: A molecular dynamics simulation study
-
Boggara, M. B.; Krishnamoorti, R. Partitioning of nonsteroidal antiinflammatory drugs in lipid membranes: a molecular dynamics simulation study Biophys. J. 2010, 98, 586-595
-
(2010)
Biophys. J.
, vol.98
, pp. 586-595
-
-
Boggara, M.B.1
Krishnamoorti, R.2
-
50
-
-
84877104063
-
Drug permeability prediction using PMF method
-
Meng, F.; Xu, W. Drug permeability prediction using PMF method J. Mol. Model. 2013, 19, 991-997
-
(2013)
J. Mol. Model.
, vol.19
, pp. 991-997
-
-
Meng, F.1
Xu, W.2
-
51
-
-
84864031542
-
Mechanism for translocation of fluoroquinolones across lipid membranes
-
Cramariuc, O.; Rog, T.; Javanainen, M.; Monticelli, L.; Polishchuk, A. V.; Vattulainen, I. Mechanism for translocation of fluoroquinolones across lipid membranes Biochim. Biophys. Acta, Biomembr. 2012, 1818, 2563-2571
-
(2012)
Biochim. Biophys. Acta, Biomembr.
, vol.1818
, pp. 2563-2571
-
-
Cramariuc, O.1
Rog, T.2
Javanainen, M.3
Monticelli, L.4
Polishchuk, A.V.5
Vattulainen, I.6
-
52
-
-
84873630396
-
Binding of serotonin to lipid membranes
-
Peters, G. H.; Wang, C.; Cruys-Bagger, N.; Velardez, G. F.; Madsen, J. J.; Westh, P. Binding of serotonin to lipid membranes J. Am. Chem. Soc. 2013, 135, 2164-2171
-
(2013)
J. Am. Chem. Soc.
, vol.135
, pp. 2164-2171
-
-
Peters, G.H.1
Wang, C.2
Cruys-Bagger, N.3
Velardez, G.F.4
Madsen, J.J.5
Westh, P.6
-
53
-
-
84874640546
-
How warfarin's structural diversity influences its phospholipid bilayer membrane permeation
-
Karlsson, B. C. G.; Olsson, G. D.; Friedman, R.; Rosengren, A. M.; Henschel, H.; Nicholls, I. A. How warfarin's structural diversity influences its phospholipid bilayer membrane permeation J. Phys. Chem. B 2013, 117, 2384-2395
-
(2013)
J. Phys. Chem. B
, vol.117
, pp. 2384-2395
-
-
Karlsson, B.C.G.1
Olsson, G.D.2
Friedman, R.3
Rosengren, A.M.4
Henschel, H.5
Nicholls, I.A.6
-
54
-
-
79954551480
-
Functional group dependence of solute partitioning to various locations within a DOPC bilayer: A comparison of molecular dynamics simulations with experiment
-
Tejwani, R. W.; Davis, M. E.; Anderson, B. D.; Stouch, T. R. Functional group dependence of solute partitioning to various locations within a DOPC bilayer: a comparison of molecular dynamics simulations with experiment J. Pharm. Sci. 2011, 100, 2136-2146
-
(2011)
J. Pharm. Sci.
, vol.100
, pp. 2136-2146
-
-
Tejwani, R.W.1
Davis, M.E.2
Anderson, B.D.3
Stouch, T.R.4
-
55
-
-
84859589861
-
Convergence of free energy profile of coumarin in lipid bilayer
-
Paloncýová, M.; Berka, K.; Otyepka, M. Convergence of free energy profile of coumarin in lipid bilayer J. Chem. Theory Comput. 2012, 8, 1200-1211
-
(2012)
J. Chem. Theory Comput.
, vol.8
, pp. 1200-1211
-
-
Paloncýová, M.1
Berka, K.2
Otyepka, M.3
-
56
-
-
72149121112
-
Location, tilt, and binding: A molecular dynamics study of voltage-sensitive dyes in biomembranes
-
Hinner, M. J.; Marrink, S.-J.; de Vries, A. H. Location, tilt, and binding: a molecular dynamics study of voltage-sensitive dyes in biomembranes J. Phys. Chem. B 2009, 113, 15807-15819
-
(2009)
J. Phys. Chem. B
, vol.113
, pp. 15807-15819
-
-
Hinner, M.J.1
Marrink, S.-J.2
De Vries, A.H.3
-
57
-
-
77958502212
-
Partitioning and localization of environment-sensitive 2-(2′-pyridyl)- and 2-(2′-pyrimidyl)-indoles in lipid membranes: A joint refinement using fluorescence measurements and molecular dynamics simulations
-
Kyrychenko, A.; Wu, F.; Thummel, R. P.; Waluk, J.; Ladokhin, A. S. Partitioning and localization of environment-sensitive 2-(2′-pyridyl)- and 2-(2′-pyrimidyl)-indoles in lipid membranes: a joint refinement using fluorescence measurements and molecular dynamics simulations J. Phys. Chem. B 2010, 114, 13574-13584
-
(2010)
J. Phys. Chem. B
, vol.114
, pp. 13574-13584
-
-
Kyrychenko, A.1
Wu, F.2
Thummel, R.P.3
Waluk, J.4
Ladokhin, A.S.5
-
58
-
-
84856555684
-
Positioning of antioxidant quercetin and its metabolites in lipid bilayer membranes: Implication for their lipid-peroxidation inhibition
-
Košinová, P.; Berka, K.; Wykes, M.; Otyepka, M.; Trouillas, P. Positioning of antioxidant quercetin and its metabolites in lipid bilayer membranes: implication for their lipid-peroxidation inhibition J. Phys. Chem. B 2012, 116, 1309-1318
-
(2012)
J. Phys. Chem. B
, vol.116
, pp. 1309-1318
-
-
Košinová, P.1
Berka, K.2
Wykes, M.3
Otyepka, M.4
Trouillas, P.5
-
59
-
-
49649089223
-
Poly(amidoamine) dendrimers on lipid bilayers I: Free energy and conformation of binding
-
Kelly, C. V.; Leroueil, P. R.; Nett, E. K.; Wereszczynski, J. M.; Baker, J. R., Jr.; Orr, B. G.; Banaszak Holl, M. M.; Andricioaei, I. Poly(amidoamine) dendrimers on lipid bilayers I: free energy and conformation of binding J. Phys. Chem. B 2008, 112, 9337-9345
-
(2008)
J. Phys. Chem. B
, vol.112
, pp. 9337-9345
-
-
Kelly, C.V.1
Leroueil, P.R.2
Nett, E.K.3
Wereszczynski, J.M.4
Baker, Jr.J.R.5
Orr, B.G.6
Banaszak Holl, M.M.7
Andricioaei, I.8
-
60
-
-
35448968223
-
Computational modeling of poly(alkylthiophene) conductive polymer insertion into phospholipid bilayers
-
Widge, A. S.; Matsuoka, Y.; Kurnikova, M. Computational modeling of poly(alkylthiophene) conductive polymer insertion into phospholipid bilayers Langmuir 2007, 23, 10672-10681
-
(2007)
Langmuir
, vol.23
, pp. 10672-10681
-
-
Widge, A.S.1
Matsuoka, Y.2
Kurnikova, M.3
-
61
-
-
58149149337
-
Molecular dynamics simulation study of a pulmonary surfactant film interacting with a carbonaceous nanoparticle
-
Choe, S.; Chang, R.; Jeon, J.; Violi, A. Molecular dynamics simulation study of a pulmonary surfactant film interacting with a carbonaceous nanoparticle Biophys. J. 2008, 95, 4102-4114
-
(2008)
Biophys. J.
, vol.95
, pp. 4102-4114
-
-
Choe, S.1
Chang, R.2
Jeon, J.3
Violi, A.4
-
62
-
-
43649094583
-
Distribution of amino acids in a lipid bilayer from computer simulations
-
MacCallum, J. L.; Bennett, W. F. D.; Tieleman, D. P. Distribution of amino acids in a lipid bilayer from computer simulations Biophys. J. 2008, 94, 3393-3404
-
(2008)
Biophys. J.
, vol.94
, pp. 3393-3404
-
-
MacCallum, J.L.1
Bennett, W.F.D.2
Tieleman, D.P.3
-
63
-
-
34247626293
-
Partitioning of amino acid side chains into lipid bilayers: Results from computer simulations and comparison to experiment
-
MacCallum, J. L.; Bennett, W. F. D.; Tieleman, D. P. Partitioning of amino acid side chains into lipid bilayers: results from computer simulations and comparison to experiment J. Gen. Physiol. 2007, 129, 371-377
-
(2007)
J. Gen. Physiol.
, vol.129
, pp. 371-377
-
-
MacCallum, J.L.1
Bennett, W.F.D.2
Tieleman, D.P.3
-
64
-
-
0037039619
-
Interaction of tryptophan analogs with POPC lipid bilayers investigated by molecular dynamics calculations
-
Grossfield, A.; Woolf, T. B. Interaction of tryptophan analogs with POPC lipid bilayers investigated by molecular dynamics calculations Langmuir 2002, 18, 198-210
-
(2002)
Langmuir
, vol.18
, pp. 198-210
-
-
Grossfield, A.1
Woolf, T.B.2
-
65
-
-
50549097744
-
Assessing atomistic and coarse-grained force fields for protein-lipid interactions: The formidable challenge of an ionizable side chain in a membrane
-
Vorobyov, I.; Li, L.; Allen, T. W. Assessing atomistic and coarse-grained force fields for protein-lipid interactions: the formidable challenge of an ionizable side chain in a membrane J. Phys. Chem. B 2008, 112, 9588-9602
-
(2008)
J. Phys. Chem. B
, vol.112
, pp. 9588-9602
-
-
Vorobyov, I.1
Li, L.2
Allen, T.W.3
-
66
-
-
50549085702
-
Potential of mean force and pKa profile calculation for a lipid membrane-exposed arginine side chain
-
Li, L.; Vorobyov, I.; Allen, T. Potential of mean force and pKa profile calculation for a lipid membrane-exposed arginine side chain J. Phys. Chem. B 2008, 112, 9574-9587
-
(2008)
J. Phys. Chem. B
, vol.112
, pp. 9574-9587
-
-
Li, L.1
Vorobyov, I.2
Allen, T.3
-
67
-
-
39749132236
-
Position-resolved free energy of solvation for amino acids in lipid membranes from molecular dynamics simulations
-
Johansson, A. C. V.; Lindahl, E. Position-resolved free energy of solvation for amino acids in lipid membranes from molecular dynamics simulations Proteins 2008, 70, 1332-1344
-
(2008)
Proteins
, vol.70
, pp. 1332-1344
-
-
Johansson, A.C.V.1
Lindahl, E.2
-
68
-
-
39749160987
-
Correction to the article "position-resolved free energy of solvation for amino acids in lipid membranes from molecular dynamics simulations"
-
Johansson, A. C. V.; Lindahl, E. Correction to the article "Position-resolved free energy of solvation for amino acids in lipid membranes from molecular dynamics simulations" Proteins 2008, 70, 1655-1656
-
(2008)
Proteins
, vol.70
, pp. 1655-1656
-
-
Johansson, A.C.V.1
Lindahl, E.2
-
69
-
-
84875803167
-
Free energetics and the role of water in the permeation of methyl guanidinium across the bilayer-water interface: Insights from molecular dynamics simulations using charge equilibration potentials
-
Ou, S.; Lucas, T. R.; Zhong, Y.; Bauer, B. A.; Hu, Y.; Patel, S. Free energetics and the role of water in the permeation of methyl guanidinium across the bilayer-water interface: insights from molecular dynamics simulations using charge equilibration potentials J. Phys. Chem. B 2013, 117, 3578-3592
-
(2013)
J. Phys. Chem. B
, vol.117
, pp. 3578-3592
-
-
Ou, S.1
Lucas, T.R.2
Zhong, Y.3
Bauer, B.A.4
Hu, Y.5
Patel, S.6
-
70
-
-
84858009825
-
Unassisted transport of N-acetyl-l-tryptophanamide through membrane: Experiment and simulation of kinetics
-
Cardenas, A. E.; Jas, G. S.; DeLeon, K. Y.; Hegefeld, W. A.; Kuczera, K.; Elber, R. Unassisted transport of N-acetyl-l-tryptophanamide through membrane: experiment and simulation of kinetics J. Phys. Chem. B 2012, 116, 2739-2750
-
(2012)
J. Phys. Chem. B
, vol.116
, pp. 2739-2750
-
-
Cardenas, A.E.1
Jas, G.S.2
Deleon, K.Y.3
Hegefeld, W.A.4
Kuczera, K.5
Elber, R.6
-
71
-
-
51849162488
-
Thermodynamics of peptide insertion and aggregation in a lipid bilayer
-
Babakhani, A.; Gorfe, A. A.; Kim, J. E.; McCammon, J. A. Thermodynamics of peptide insertion and aggregation in a lipid bilayer J. Phys. Chem. B 2008, 112, 10528-10534
-
(2008)
J. Phys. Chem. B
, vol.112
, pp. 10528-10534
-
-
Babakhani, A.1
Gorfe, A.A.2
Kim, J.E.3
McCammon, J.A.4
-
72
-
-
84872818385
-
Free energy of translocating an arginine-rich cell-penetrating peptide across a lipid bilayer suggests pore formation
-
Huang, K.; García, A. E. Free energy of translocating an arginine-rich cell-penetrating peptide across a lipid bilayer suggests pore formation Biophys. J. 2013, 104, 412-420
-
(2013)
Biophys. J.
, vol.104
, pp. 412-420
-
-
Huang, K.1
García, A.E.2
-
73
-
-
77958460527
-
Sequence-dependent interaction of β-peptides with membranes
-
Mondal, J.; Zhu, X.; Cui, Q.; Yethiraj, A. Sequence-dependent interaction of β-peptides with membranes J. Phys. Chem. B 2010, 114, 13585-13592
-
(2010)
J. Phys. Chem. B
, vol.114
, pp. 13585-13592
-
-
Mondal, J.1
Zhu, X.2
Cui, Q.3
Yethiraj, A.4
-
74
-
-
84858325640
-
Free energy difference in indolicidin attraction to eukaryotic and prokaryotic model cell membranes
-
Yeh, I.-C.; Ripoll, D. R.; Wallqvist, A. Free energy difference in indolicidin attraction to eukaryotic and prokaryotic model cell membranes J. Phys. Chem. B 2012, 116, 3387-3396
-
(2012)
J. Phys. Chem. B
, vol.116
, pp. 3387-3396
-
-
Yeh, I.-C.1
Ripoll, D.R.2
Wallqvist, A.3
-
75
-
-
77749304229
-
Free energy profile of the interaction between a monomer or a dimer of protegrin-1 in a specific binding orientation and a model lipid bilayer
-
Vivcharuk, V.; Kaznessis, Y. Free energy profile of the interaction between a monomer or a dimer of protegrin-1 in a specific binding orientation and a model lipid bilayer J. Phys. Chem. B 2010, 114, 2790-2797
-
(2010)
J. Phys. Chem. B
, vol.114
, pp. 2790-2797
-
-
Vivcharuk, V.1
Kaznessis, Y.2
-
76
-
-
84865318587
-
Binding and reorientation of melittin in a POPC bilayer: Computer simulations
-
Irudayam, S. J.; Berkowitz, M. L. Binding and reorientation of melittin in a POPC bilayer: computer simulations Biochim. Biophys. Acta, Biomembr. 2012, 1818, 2975-2981
-
(2012)
Biochim. Biophys. Acta, Biomembr.
, vol.1818
, pp. 2975-2981
-
-
Irudayam, S.J.1
Berkowitz, M.L.2
-
77
-
-
77954371031
-
Revisiting hydrophobic mismatch with free energy simulation studies of transmembrane helix tilt and rotation
-
Kim, T.; Im, W. Revisiting hydrophobic mismatch with free energy simulation studies of transmembrane helix tilt and rotation Biophys. J. 2010, 99, 175-183
-
(2010)
Biophys. J.
, vol.99
, pp. 175-183
-
-
Kim, T.1
Im, W.2
-
78
-
-
84875274207
-
Effect of gating modifier toxins on membrane thickness: Implications for toxin effect on gramicidin and mechanosensitive channels
-
Chen, R.; Chung, S.-H. Effect of gating modifier toxins on membrane thickness: implications for toxin effect on gramicidin and mechanosensitive channels Toxins 2013, 5, 456-471
-
(2013)
Toxins
, vol.5
, pp. 456-471
-
-
Chen, R.1
Chung, S.-H.2
-
79
-
-
61549084018
-
Interaction between amyloid-β (1-42) peptide and phospholipid bilayers: A molecular dynamics study
-
Davis, C. H.; Berkowitz, M. L. Interaction between amyloid-β (1-42) peptide and phospholipid bilayers: a molecular dynamics study Biophys. J. 2009, 96, 785-797
-
(2009)
Biophys. J.
, vol.96
, pp. 785-797
-
-
Davis, C.H.1
Berkowitz, M.L.2
-
80
-
-
84871752186
-
The role of tryptophan side chains in membrane protein anchoring and hydrophobic mismatch
-
de Jesus, A. J.; Allen, T. W. The role of tryptophan side chains in membrane protein anchoring and hydrophobic mismatch. Biochim. Biophys. Acta, Biomembr. 2013, 1828, 864-876.
-
(2013)
Biochim. Biophys. Acta, Biomembr.
, vol.1828
, pp. 864-876
-
-
De Jesus, A.J.1
Allen, T.W.2
-
81
-
-
34247633528
-
On the thermodynamic stability of a charged arginine side chain in a transmembrane helix
-
Dorairaj, S.; Allen, T. W. On the thermodynamic stability of a charged arginine side chain in a transmembrane helix Proc. Natl. Acad. Sci. U. S. A. 2007, 104, 4943-4948
-
(2007)
Proc. Natl. Acad. Sci. U. S. A.
, vol.104
, pp. 4943-4948
-
-
Dorairaj, S.1
Allen, T.W.2
-
82
-
-
0034294024
-
Multidimensional replica-exchange method for free-energy calculations
-
Sugita, Y.; Kitao, A.; Okamoto, Y. Multidimensional replica-exchange method for free-energy calculations J. Chem. Phys. 2000, 113, 6042-6051
-
(2000)
J. Chem. Phys.
, vol.113
, pp. 6042-6051
-
-
Sugita, Y.1
Kitao, A.2
Okamoto, Y.3
-
83
-
-
46849085002
-
Equilibrium exchange enhances the convergence rate of umbrella sampling
-
Neale, C.; Rodinger, T.; Pomès, R. Equilibrium exchange enhances the convergence rate of umbrella sampling Chem. Phys. Lett. 2008, 460, 375-381
-
(2008)
Chem. Phys. Lett.
, vol.460
, pp. 375-381
-
-
Neale, C.1
Rodinger, T.2
Pomès, R.3
-
84
-
-
84863272836
-
Transmembrane helix assembly by window exchange umbrella sampling
-
Park, S.; Kim, T.; Im, W. Transmembrane helix assembly by window exchange umbrella sampling Phys. Rev. Lett. 2012, 108, 108102
-
(2012)
Phys. Rev. Lett.
, vol.108
, pp. 108102
-
-
Park, S.1
Kim, T.2
Im, W.3
-
85
-
-
55949089646
-
Rapid free energy calculation of peptide self-assembly by REMD umbrella sampling
-
Wolf, M. G.; Jongejan, J. A.; Laman, J. D.; de Leeuw, S. W. Rapid free energy calculation of peptide self-assembly by REMD umbrella sampling J. Phys. Chem. B 2008, 112, 13493-13498
-
(2008)
J. Phys. Chem. B
, vol.112
, pp. 13493-13498
-
-
Wolf, M.G.1
Jongejan, J.A.2
Laman, J.D.3
De Leeuw, S.W.4
-
86
-
-
33846106377
-
Convergence and sampling efficiency in replica exchange simulations of peptide folding in explicit solvent
-
Periole, X.; Mark, A. E. Convergence and sampling efficiency in replica exchange simulations of peptide folding in explicit solvent J. Chem. Phys. 2007, 126, 014903
-
(2007)
J. Chem. Phys.
, vol.126
, pp. 014903
-
-
Periole, X.1
Mark, A.E.2
-
87
-
-
4243819810
-
New Monte Carlo technique for studying phase transitions
-
Ferrenberg, A. M.; Swendsen, R. H. New Monte Carlo technique for studying phase transitions Phys. Rev. Lett. 1988, 61, 2635-2638
-
(1988)
Phys. Rev. Lett.
, vol.61
, pp. 2635-2638
-
-
Ferrenberg, A.M.1
Swendsen, R.H.2
-
88
-
-
0031578972
-
Parallel tempering algorithm for conformational studies of biological molecules
-
Hansmann, U. H. E. Parallel tempering algorithm for conformational studies of biological molecules Chem. Phys. Lett. 1997, 281, 140-150
-
(1997)
Chem. Phys. Lett.
, vol.281
, pp. 140-150
-
-
Hansmann, U.H.E.1
-
89
-
-
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, 141-151
-
(1999)
Chem. Phys. Lett.
, vol.314
, pp. 141-151
-
-
Sugita, Y.1
Okamoto, Y.2
-
90
-
-
0039924671
-
Monte carlo study of the interacting self-avoiding walk model in three dimensions
-
Tesi, M. C.; van Rensburg, E. J. J.; Orlandini, E.; Whittington, S. G. Monte carlo study of the interacting self-avoiding walk model in three dimensions J. Stat. Phys. 1996, 82, 155-181
-
(1996)
J. Stat. Phys.
, vol.82
, pp. 155-181
-
-
Tesi, M.C.1
Van Rensburg, E.J.J.2
Orlandini, E.3
Whittington, S.G.4
-
91
-
-
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, 1604-1608
-
(1996)
J. Phys. Soc. Jpn.
, vol.65
, pp. 1604-1608
-
-
Hukushima, K.1
Nemoto, K.2
-
92
-
-
33750970357
-
A Second Look at Canonical Sampling of Biomolecules Using Replica Exchange Simulation
-
Zuckerman, D. M.; Lyman, E. A Second Look at Canonical Sampling of Biomolecules Using Replica Exchange Simulation J. Chem. Theory Comput. 2006, 2, 1200-1202
-
(2006)
J. Chem. Theory Comput.
, vol.2
, pp. 1200-1202
-
-
Zuckerman, D.M.1
Lyman, E.2
-
93
-
-
33750970357
-
A Second Look at Canonical Sampling of Biomolecules Using Replica Exchange Simulation [J. Chem. Theory Comput. 2, 1200-1202 (2006)]
-
Zuckerman, D. M.; Lyman, E. A Second Look at Canonical Sampling of Biomolecules Using Replica Exchange Simulation [J. Chem. Theory Comput. 2, 1200-1202 (2006)] J. Chem. Theory Comput. 2006, 2, 1693-1693
-
(2006)
J. Chem. Theory Comput.
, vol.2
, pp. 1693-1693
-
-
Zuckerman, D.M.1
Lyman, E.2
-
94
-
-
0025285274
-
Positively charged residues are important determinants of membrane protein topology
-
Dalbey, R. E. Positively charged residues are important determinants of membrane protein topology Trends Biochem. Sci. 1990, 15, 253-257
-
(1990)
Trends Biochem. Sci.
, vol.15
, pp. 253-257
-
-
Dalbey, R.E.1
-
95
-
-
0025059797
-
The role of charged amino acids in the localization of secreted and membrane proteins
-
Boyd, D.; Beckwith, J. The role of charged amino acids in the localization of secreted and membrane proteins Cell 1990, 62, 1031-1033
-
(1990)
Cell
, vol.62
, pp. 1031-1033
-
-
Boyd, D.1
Beckwith, J.2
-
96
-
-
0024372724
-
Positively charged amino acid residues can act as topogenic determinants in membrane proteins
-
Boyd, D.; Beckwith, J. Positively charged amino acid residues can act as topogenic determinants in membrane proteins Proc. Natl. Acad. Sci. U. S. A. 1989, 86, 9446-9450
-
(1989)
Proc. Natl. Acad. Sci. U. S. A.
, vol.86
, pp. 9446-9450
-
-
Boyd, D.1
Beckwith, J.2
-
97
-
-
79955650131
-
A look at arginine in membranes
-
Hristova, K.; Wimley, W. C. A look at arginine in membranes J. Membr. Biol. 2011, 239, 49-56
-
(2011)
J. Membr. Biol.
, vol.239
, pp. 49-56
-
-
Hristova, K.1
Wimley, W.C.2
-
98
-
-
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, 435-447
-
(2008)
J. Chem. Theory Comput.
, vol.4
, pp. 435-447
-
-
Hess, B.1
Kutzner, C.2
Van Der Spoel, D.3
Lindahl, E.4
-
99
-
-
0004016501
-
Comparison of simple potential functions for simulating liquid water
-
Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. Comparison of simple potential functions for simulating liquid water J. Chem. Phys. 1983, 79, 926-935
-
(1983)
J. Chem. Phys.
, vol.79
, pp. 926-935
-
-
Jorgensen, W.L.1
Chandrasekhar, J.2
Madura, J.D.3
Impey, R.W.4
Klein, M.L.5
-
100
-
-
0030999097
-
Molecular dynamics simulations of a fluid bilayer of dipalmitoylphosphatidylcholine at full hydration, constant pressure, and constant temperature
-
Berger, O.; Edholm, O.; Jähnig, F. Molecular dynamics simulations of a fluid bilayer of dipalmitoylphosphatidylcholine at full hydration, constant pressure, and constant temperature Biophys. J. 1997, 72, 2002-2013
-
(1997)
Biophys. J.
, vol.72
, pp. 2002-2013
-
-
Berger, O.1
Edholm, O.2
Jähnig, F.3
-
101
-
-
0029912748
-
Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids
-
Jorgensen, W. L.; Maxwell, D. S.; Tirado-Rives, J. Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids J. Am. Chem. Soc. 1996, 118, 11225-11236
-
(1996)
J. Am. Chem. Soc.
, vol.118
, pp. 11225-11236
-
-
Jorgensen, W.L.1
Maxwell, D.S.2
Tirado-Rives, J.3
-
102
-
-
0035913529
-
Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides
-
Kaminski, G. A.; Friesner, R. A.; Tirado-Rives, J.; Jorgensen, W. L. Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides J. Phys. Chem. B 2001, 105, 6474-6487
-
(2001)
J. Phys. Chem. B
, vol.105
, pp. 6474-6487
-
-
Kaminski, G.A.1
Friesner, R.A.2
Tirado-Rives, J.3
Jorgensen, W.L.4
-
103
-
-
0001585978
-
Improving efficiency of large time-scale molecular dynamics simulations of hydrogen-rich systems
-
Feenstra, K. A.; Hess, B.; Berendsen, H. J. C. Improving efficiency of large time-scale molecular dynamics simulations of hydrogen-rich systems J. Comput. Chem. 1999, 20, 786-798
-
(1999)
J. Comput. Chem.
, vol.20
, pp. 786-798
-
-
Feenstra, K.A.1
Hess, B.2
Berendsen, H.J.C.3
-
104
-
-
77749320417
-
An iris-like mechanism of pore dilation in the CorA magnesium transport system
-
Chakrabarti, N.; Neale, C.; Payandeh, J.; Pai, E. F.; Pomès, R. An iris-like mechanism of pore dilation in the CorA magnesium transport system Biophys. J. 2010, 98, 784-792
-
(2010)
Biophys. J.
, vol.98
, pp. 784-792
-
-
Chakrabarti, N.1
Neale, C.2
Payandeh, J.3
Pai, E.F.4
Pomès, R.5
-
105
-
-
84986440341
-
Settle: An analytical version of the SHAKE and RATTLE algorithm for rigid water models
-
Miyamoto, S.; Kollman, P. A. Settle: An analytical version of the SHAKE and RATTLE algorithm for rigid water models J. Comput. Chem. 1992, 13, 952-962
-
(1992)
J. Comput. Chem.
, vol.13
, pp. 952-962
-
-
Miyamoto, S.1
Kollman, P.A.2
-
106
-
-
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, 116-122
-
(2008)
J. Chem. Theory Comput.
, vol.4
, pp. 116-122
-
-
Hess, B.1
-
107
-
-
0032951553
-
Alamethicin helices in a bilayer and in solution: Molecular dynamics simulations
-
Tieleman, D. P.; Sansom, M. S. P.; Berendsen, H. J. C. Alamethicin helices in a bilayer and in solution: molecular dynamics simulations Biophys. J. 1999, 76, 40-49
-
(1999)
Biophys. J.
, vol.76
, pp. 40-49
-
-
Tieleman, D.P.1
Sansom, M.S.P.2
Berendsen, H.J.C.3
-
108
-
-
33846823909
-
Particle mesh Ewald: An N •log(N) method for Ewald sums in large systems
-
Darden, T.; York, D.; Pedersen, L. Particle mesh Ewald: An N •log(N) method for Ewald sums in large systems J. Chem. Phys. 1993, 98, 10089-10092
-
(1993)
J. Chem. Phys.
, vol.98
, pp. 10089-10092
-
-
Darden, T.1
York, D.2
Pedersen, L.3
-
109
-
-
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, 8577-8593
-
(1995)
J. Chem. Phys.
, vol.103
, pp. 8577-8593
-
-
Essmann, U.1
Perera, L.2
Berkowitz, M.L.3
Darden, T.4
Lee, H.5
Pedersen, L.G.6
-
110
-
-
33750587438
-
Molecular dynamics with coupling to an external bath
-
Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; DiNola, A.; Haak, J. R. Molecular dynamics with coupling to an external bath J. Chem. Phys. 1984, 81, 3684-3690
-
(1984)
J. Chem. Phys.
, vol.81
, pp. 3684-3690
-
-
Berendsen, H.J.C.1
Postma, J.P.M.2
Van Gunsteren, W.F.3
Dinola, A.4
Haak, J.R.5
-
111
-
-
84943200457
-
A leap-frog algorithm for stochastic dynamics
-
van Gunsteren, W. F.; Berendsen, H. J. C. A leap-frog algorithm for stochastic dynamics Mol. Sim. 1988, 1, 173-185
-
(1988)
Mol. Sim.
, vol.1
, pp. 173-185
-
-
Van Gunsteren, W.F.1
Berendsen, H.J.C.2
-
112
-
-
33947139278
-
Setting up and running molecular dynamics simulations of membrane proteins
-
Kandt, C.; Ash, W. L.; Tieleman, D. P. Setting up and running molecular dynamics simulations of membrane proteins Methods 2007, 41, 475-488
-
(2007)
Methods
, vol.41
, pp. 475-488
-
-
Kandt, C.1
Ash, W.L.2
Tieleman, D.P.3
-
114
-
-
84986519238
-
The weighted histogram analysis method for free-energy calculations on biomolecules. I. The method
-
Kumar, S.; Rosenberg, J. M.; Bouzida, D.; Swendsen, R. H.; Kollman, P. A. The weighted histogram analysis method for free-energy calculations on biomolecules. I. The method J. Comput. Chem. 1992, 13, 1011-1021
-
(1992)
J. Comput. Chem.
, vol.13
, pp. 1011-1021
-
-
Kumar, S.1
Rosenberg, J.M.2
Bouzida, D.3
Swendsen, R.H.4
Kollman, P.A.5
-
115
-
-
0029669955
-
Free-energy determinants of alpha-helix insertion into lipid bilayers
-
Ben-Tal, N.; Ben-Shaul, A.; Nicholls, A.; Honig, B. Free-energy determinants of alpha-helix insertion into lipid bilayers Biophys. J. 1996, 70, 1803-1812
-
(1996)
Biophys. J.
, vol.70
, pp. 1803-1812
-
-
Ben-Tal, N.1
Ben-Shaul, A.2
Nicholls, A.3
Honig, B.4
-
116
-
-
77955578745
-
A note on the standard state's binding free energy
-
General, I. J. A note on the standard state's binding free energy J. Chem. Theory Comput. 2010, 6, 2520-2524
-
(2010)
J. Chem. Theory Comput.
, vol.6
, pp. 2520-2524
-
-
General, I.J.1
-
117
-
-
36549102647
-
Error estimates on averages of correlated data
-
Flyvbjerg, H.; Petersen, H. G. Error estimates on averages of correlated data J. Chem. Phys. 1989, 91, 461-466
-
(1989)
J. Chem. Phys.
, vol.91
, pp. 461-466
-
-
Flyvbjerg, H.1
Petersen, H.G.2
-
118
-
-
33846202602
-
Distributed replica sampling
-
Rodinger, T.; Howell, P. L.; Pomès, R. Distributed replica sampling J. Chem. Theory Comput. 2006, 2, 725-731
-
(2006)
J. Chem. Theory Comput.
, vol.2
, pp. 725-731
-
-
Rodinger, T.1
Howell, P.L.2
Pomès, R.3
-
119
-
-
0011757586
-
Statistical analysis of simulations: Data correlations and error estimation
-
In; Grotendorst, J. Marx, D. Murmatsu, A. John von Neumann Institute for Computing: Jülich, Germany
-
Janke, W. Statistical analysis of simulations: data correlations and error estimation. In Quantum Simulations of Complex Many-Body Systems: From Theory to Algorithms; Grotendorst, J.; Marx, D.; Murmatsu, A., Eds.; John von Neumann Institute for Computing: Jülich, Germany, 2002; Vol. 10, pp 423-445.
-
(2002)
Quantum Simulations of Complex Many-Body Systems: From Theory to Algorithms
, vol.10
, pp. 423-445
-
-
Janke, W.1
-
120
-
-
80051613692
-
Block Covariance Overlap Method and Convergence in Molecular Dynamics Simulation
-
Romo, T. D.; Grossfield, A. Block Covariance Overlap Method and Convergence in Molecular Dynamics Simulation J. Chem. Theory Comput. 2011, 7, 2464-2472
-
(2011)
J. Chem. Theory Comput.
, vol.7
, pp. 2464-2472
-
-
Romo, T.D.1
Grossfield, A.2
-
121
-
-
36549097253
-
The lag between the Hamiltonian and the system configuration in free energy perturbation calculations
-
Pearlman, D. A.; Kollman, P. A. The lag between the Hamiltonian and the system configuration in free energy perturbation calculations J. Chem. Phys. 1989, 91, 7831-7839
-
(1989)
J. Chem. Phys.
, vol.91
, pp. 7831-7839
-
-
Pearlman, D.A.1
Kollman, P.A.2
-
122
-
-
67649114369
-
Simultaneous escaping of explicit and hidden free energy barriers: Application of the orthogonal space random walk strategy in generalized ensemble based conformational sampling
-
Zheng, L.; Chen, M.; Yang, W. Simultaneous escaping of explicit and hidden free energy barriers: application of the orthogonal space random walk strategy in generalized ensemble based conformational sampling J. Chem. Phys. 2009, 130, 234105
-
(2009)
J. Chem. Phys.
, vol.130
, pp. 234105
-
-
Zheng, L.1
Chen, M.2
Yang, W.3
-
123
-
-
34547642319
-
Lonely arginine seeks friendly environment
-
Roux, B. Lonely arginine seeks friendly environment J. Gen. Physiol. 2007, 130, 233-236
-
(2007)
J. Gen. Physiol.
, vol.130
, pp. 233-236
-
-
Roux, B.1
-
124
-
-
38349033291
-
Is arginine charged in a membrane?
-
Li, L.; Vorobyov, I.; MacKerell, A. D.; Allen, T. W. Is arginine charged in a membrane? Biophys. J. 2008, 94, L11-L13
-
(2008)
Biophys. J.
, vol.94
-
-
Li, L.1
Vorobyov, I.2
MacKerell, A.D.3
Allen, T.W.4
-
125
-
-
43149121350
-
Does arginine remain protonated in the lipid membrane? Insights from microscopic pKa calculations
-
Yoo, J.; Cui, Q. Does arginine remain protonated in the lipid membrane? Insights from microscopic pKa calculations Biophys. J. 2008, 94, L61-L63
-
(2008)
Biophys. J.
, vol.94
-
-
Yoo, J.1
Cui, Q.2
-
126
-
-
33846050049
-
Molecular dynamics of apo-adenylate kinase: A distance replica exchange method for the free energy of conformational fluctuations
-
Lou, H.; Cukier, R. I. Molecular dynamics of apo-adenylate kinase: a distance replica exchange method for the free energy of conformational fluctuations J. Phys. Chem. B 2006, 110, 24121-24137
-
(2006)
J. Phys. Chem. B
, vol.110
, pp. 24121-24137
-
-
Lou, H.1
Cukier, R.I.2
-
127
-
-
77956574437
-
Free energy perturbation Hamiltonian replica-exchange molecular dynamics (FEP/H-REMD) for absolute ligand binding free energy calculations
-
Jiang, W.; Roux, B. t. Free energy perturbation Hamiltonian replica-exchange molecular dynamics (FEP/H-REMD) for absolute ligand binding free energy calculations J. Chem. Theory Comput. 2010, 6, 2559-2565
-
(2010)
J. Chem. Theory Comput.
, vol.6
, pp. 2559-2565
-
-
Jiang, W.1
Roux, B.R.2
-
128
-
-
80052803759
-
Computing alchemical free energy differences with Hamiltonian replica exchange molecular dynamics (H-REMD) simulations
-
Meng, Y.; Sabri Dashti, D.; Roitberg, A. E. Computing alchemical free energy differences with Hamiltonian replica exchange molecular dynamics (H-REMD) simulations J. Chem. Theory Comput. 2011, 7, 2721-2727
-
(2011)
J. Chem. Theory Comput.
, vol.7
, pp. 2721-2727
-
-
Meng, Y.1
Sabri Dashti, D.2
Roitberg, A.E.3
-
129
-
-
0346350789
-
The development of replica-exchange-based free-energy methods
-
Woods, C. J.; Essex, J. W.; King, M. A. The development of replica-exchange-based free-energy methods J. Phys. Chem. B 2003, 107, 13703-13710
-
(2003)
J. Phys. Chem. B
, vol.107
, pp. 13703-13710
-
-
Woods, C.J.1
Essex, J.W.2
King, M.A.3
-
130
-
-
54849417403
-
Calculation of absolute protein-ligand binding free energy using distributed replica sampling
-
Rodinger, T.; Howell, P. L.; Pomès, R. Calculation of absolute protein-ligand binding free energy using distributed replica sampling J. Chem. Phys. 2008, 129, 155102-12
-
(2008)
J. Chem. Phys.
, vol.129
, pp. 155102-155112
-
-
Rodinger, T.1
Howell, P.L.2
Pomès, R.3
-
131
-
-
66349093679
-
Reordering hydrogen bonds using Hamiltonian replica exchange enhances sampling of conformational changes in biomolecular systems
-
Vreede, J.; Wolf, M. G.; de Leeuw, S. W.; Bolhuis, P. G. Reordering hydrogen bonds using Hamiltonian replica exchange enhances sampling of conformational changes in biomolecular systems J. Phys. Chem. B 2009, 113, 6484-6494
-
(2009)
J. Phys. Chem. B
, vol.113
, pp. 6484-6494
-
-
Vreede, J.1
Wolf, M.G.2
De Leeuw, S.W.3
Bolhuis, P.G.4
-
132
-
-
0001320763
-
Studies on free energy calculations. I. Thermodynamic integration using a polynomial path
-
Resat, H.; Mezei, M. Studies on free energy calculations. I. Thermodynamic integration using a polynomial path J. Chem. Phys. 1993, 99, 6052-6061
-
(1993)
J. Chem. Phys.
, vol.99
, pp. 6052-6061
-
-
Resat, H.1
Mezei, M.2
-
133
-
-
34548703110
-
Alchemical free energy calculations: Ready for prime time?
-
In; Spellmeyer, D. C. Wheeler, R. Elsevier: Amsterdam
-
Shirts, M. R.; Mobley, D. L.; Chodera, J. D. Alchemical free energy calculations: ready for prime time? In Annu. Rep. Comput. Chem.; Spellmeyer, D. C.; Wheeler, R., Eds.; Elsevier: Amsterdam, 2007; Vol. 3, pp 41-59.
-
(2007)
Annu. Rep. Comput. Chem.
, vol.3
, pp. 41-59
-
-
Shirts, M.R.1
Mobley, D.L.2
Chodera, J.D.3
-
134
-
-
0034864528
-
Generalized-ensemble algorithms for molecular simulations of biopolymers
-
Mitsutake, A.; Sugita, Y.; Okamoto, Y. Generalized-ensemble algorithms for molecular simulations of biopolymers Peptide Sci. 2001, 60, 96-123
-
(2001)
Peptide Sci.
, vol.60
, pp. 96-123
-
-
Mitsutake, A.1
Sugita, Y.2
Okamoto, Y.3
-
135
-
-
0000855275
-
Replica-exchange simulated tempering method for simulations of frustrated systems
-
Mitsutake, A.; Okamoto, Y. Replica-exchange simulated tempering method for simulations of frustrated systems Chem. Phys. Lett. 2000, 332, 131-138
-
(2000)
Chem. Phys. Lett.
, vol.332
, pp. 131-138
-
-
Mitsutake, A.1
Okamoto, Y.2
-
136
-
-
23944458073
-
Replica-exchange molecular dynamics simulation of small peptide in water and in ethanol
-
Yoshida, K.; Yamaguchi, T.; Okamoto, Y. Replica-exchange molecular dynamics simulation of small peptide in water and in ethanol Chem. Phys. Lett. 2005, 412, 280-284
-
(2005)
Chem. Phys. Lett.
, vol.412
, pp. 280-284
-
-
Yoshida, K.1
Yamaguchi, T.2
Okamoto, Y.3
-
137
-
-
10844230140
-
Replica exchange molecular dynamics simulations of amyloid peptide aggregation
-
Cecchini, M.; Rao, F.; Seeber, M.; Caflisch, A. Replica exchange molecular dynamics simulations of amyloid peptide aggregation J. Chem. Phys. 2004, 121, 10748-10756
-
(2004)
J. Chem. Phys.
, vol.121
, pp. 10748-10756
-
-
Cecchini, M.1
Rao, F.2
Seeber, M.3
Caflisch, A.4
-
138
-
-
0041877561
-
Replica exchange molecular dynamics simulations of reversible folding
-
Rao, F.; Caflisch, A. Replica exchange molecular dynamics simulations of reversible folding J. Chem. Phys. 2003, 119, 4035-4042
-
(2003)
J. Chem. Phys.
, vol.119
, pp. 4035-4042
-
-
Rao, F.1
Caflisch, A.2
-
139
-
-
57749086898
-
Folding proteins by first-passage-times-optimized replica exchange
-
Nadler, W.; Meinke, J. H.; Hansmann, U. H. E. Folding proteins by first-passage-times-optimized replica exchange Phys. Rev. E 2008, 78, 061905
-
(2008)
Phys. Rev. e
, vol.78
, pp. 061905
-
-
Nadler, W.1
Meinke, J.H.2
Hansmann, U.H.E.3
-
140
-
-
20844439932
-
Selection of temperature intervals for parallel-tempering simulations
-
Kone, A.; Kofke, D. A. Selection of temperature intervals for parallel-tempering simulations J. Chem. Phys. 2005, 122, 206101-2
-
(2005)
J. Chem. Phys.
, vol.122
, pp. 206101-206102
-
-
Kone, A.1
Kofke, D.A.2
-
141
-
-
34547139358
-
Optimized parallel tempering simulations of proteins
-
Trebst, S.; Troyer, M.; Hansmann, U. H. E. Optimized parallel tempering simulations of proteins J. Chem. Phys. 2006, 124, 174903-6
-
(2006)
J. Chem. Phys.
, vol.124
, pp. 174903-174906
-
-
Trebst, S.1
Troyer, M.2
Hansmann, U.H.E.3
-
142
-
-
40549083345
-
Satisfying the fluctuation theorem in free-energy calculations with Hamiltonian replica exchange
-
Wyczalkowski, M. A.; Pappu, R. V. Satisfying the fluctuation theorem in free-energy calculations with Hamiltonian replica exchange Phys. Rev. E 2008, 77, 026104
-
(2008)
Phys. Rev. e
, vol.77
, pp. 026104
-
-
Wyczalkowski, M.A.1
Pappu, R.V.2
-
143
-
-
18844362955
-
Folding is not required for bilayer insertion: Replica exchange simulations of an alpha-helical peptide with an explicit lipid bilayer
-
Nymeyer, H.; Woolf, T. B.; García, A. E. Folding is not required for bilayer insertion: replica exchange simulations of an alpha-helical peptide with an explicit lipid bilayer Proteins 2005, 59, 783-790
-
(2005)
Proteins
, vol.59
, pp. 783-790
-
-
Nymeyer, H.1
Woolf, T.B.2
García, A.E.3
-
144
-
-
0036229927
-
Simulations of membranes and other interfacial systems using P21 and Pc periodic boundary conditions
-
Dolan, E. A.; Venable, R. M.; Pastor, R. W.; Brooks, B. R. Simulations of membranes and other interfacial systems using P21 and Pc periodic boundary conditions Biophys. J. 2002, 82, 2317-2325
-
(2002)
Biophys. J.
, vol.82
, pp. 2317-2325
-
-
Dolan, E.A.1
Venable, R.M.2
Pastor, R.W.3
Brooks, B.R.4
-
145
-
-
79952426683
-
SciNet: Lessons learned from building a power-efficient top-20 system and data centre
-
Loken, C.; Gruner, D.; Groer, L.; Peltier, R.; Bunn, N.; Craig, M.; Henriques, T.; Dempsey, J.; Yu, C.-H.; Chen, J.; Dursi, L. J.; Chong, J.; Northrup, S.; Pinto, J.; Knecht, N.; Van Zon, R. SciNet: lessons learned from building a power-efficient top-20 system and data centre J. Phys. Conf. Ser. 2010, 256, 012026
-
(2010)
J. Phys. Conf. Ser.
, vol.256
, pp. 012026
-
-
Loken, C.1
Gruner, D.2
Groer, L.3
Peltier, R.4
Bunn, N.5
Craig, M.6
Henriques, T.7
Dempsey, J.8
Yu, C.-H.9
Chen, J.10
Dursi, L.J.11
Chong, J.12
Northrup, S.13
Pinto, J.14
Knecht, N.15
Van Zon, R.16
-
146
-
-
0029878720
-
VMD: Visual molecular dynamics
-
Humphrey, W.; Dalke, A.; Schulten, K. VMD: visual molecular dynamics J. Mol. Graphics 1996, 14, 33-38
-
(1996)
J. Mol. Graphics
, vol.14
, pp. 33-38
-
-
Humphrey, W.1
Dalke, A.2
Schulten, K.3
-
147
-
-
84882352834
-
-
gnuplot 4.4: in interactive plotting program. (accessed March 20)
-
Williams, T.; Kelly, C. gnuplot 4.4: in interactive plotting program. http://gnuplot.sourceforge.net/ (accessed March 20, 2012).
-
(2012)
-
-
Williams, T.1
Kelly, C.2
|