-
1
-
-
33646170214
-
Simulationbased methods for interpreting x-ray data from lipid bilayers
-
Klauda, J. B.; Kučerka, N.; Brooks, B. R.; Pastor, R. W.; Nagle, J. F. Simulationbased methods for interpreting x-ray data from lipid bilayers Biophys. J. 2006, 90, 2796-2807
-
(2006)
Biophys. J.
, vol.90
, pp. 2796-2807
-
-
Klauda, J.B.1
Kučerka, N.2
Brooks, B.R.3
Pastor, R.W.4
Nagle, J.F.5
-
2
-
-
33846959867
-
Conformational analysis of lipid molecules by self-organizing maps
-
Murtola, T.; Kupiainen, M.; Falck, E.; Vattulainen, I. Conformational analysis of lipid molecules by self-organizing maps. J. Chem. Phys. 2007, 126.
-
(2007)
J. Chem. Phys.
, vol.126
-
-
Murtola, T.1
Kupiainen, M.2
Falck, E.3
Vattulainen, I.4
-
3
-
-
0000254361
-
A Voronoi analysis of lipid area fluctuation in a bilayer
-
Shinoda, W.; Okazaki, S. A Voronoi analysis of lipid area fluctuation in a bilayer J. Chem. Phys. 1998, 109, 1517
-
(1998)
J. Chem. Phys.
, vol.109
, pp. 1517
-
-
Shinoda, W.1
Okazaki, S.2
-
4
-
-
33744958820
-
Lateral diffusion and percolation in membranes
-
Sung, B. J.; Yethiraj, A. Lateral diffusion and percolation in membranes Phys. Rev. Lett. 2006, 96, 228103-228106
-
(2006)
Phys. Rev. Lett.
, vol.96
, pp. 228103-228106
-
-
Sung, B.J.1
Yethiraj, A.2
-
5
-
-
37349011230
-
The dynamic orientation of membrane-bound peptides: Bridging simulations and experiments
-
Esteban-Martín, S.; Salgado, J. The dynamic orientation of membrane-bound peptides: bridging simulations and experiments Biophys. J. 2007, 93, 4278-4288
-
(2007)
Biophys. J.
, vol.93
, pp. 4278-4288
-
-
Esteban-Martín, S.1
Salgado, J.2
-
7
-
-
84927514013
-
Nouvelles applications des paramètres continus à la théorie des formes quadratiques. Deuxième mémoire. Recherches sur les parallélloèdres primitifs
-
Voronoi, G. Nouvelles applications des paramètres continus à la théorie des formes quadratiques. Deuxième mémoire. Recherches sur les parallélloèdres primitifs J. Reine Angew. Math. 2009, 1908, 198-287
-
(2009)
J. Reine Angew. Math.
, vol.1908
, pp. 198-287
-
-
Voronoi, G.1
-
8
-
-
0041706333
-
An algorithm to describe molecular scale rugged surfaces and its application to the study of a water/lipid bilayer interface
-
Pandit, S. A.; Bostick, D.; Berkowitz, M. An algorithm to describe molecular scale rugged surfaces and its application to the study of a water/lipid bilayer interface J. Chem. Phys. 2003, 119, 2199-2205
-
(2003)
J. Chem. Phys.
, vol.119
, pp. 2199-2205
-
-
Pandit, S.A.1
Bostick, D.2
Berkowitz, M.3
-
9
-
-
16344378112
-
Simulation of the Early Stages of Nano-Domain Formation in Mixed Bilayers of Sphingomyelin, Cholesterol, and Dioleylphosphatidylcholine
-
Pandit, S. A.; Jakobsson, E.; Scott, H. L. Simulation of the Early Stages of Nano-Domain Formation in Mixed Bilayers of Sphingomyelin, Cholesterol, and Dioleylphosphatidylcholine Biophys. J. 2004, 87, 3312-3322
-
(2004)
Biophys. J.
, vol.87
, pp. 3312-3322
-
-
Pandit, S.A.1
Jakobsson, E.2
Scott, H.L.3
-
10
-
-
34548059458
-
Molecular dynamics investigation of the structural properties of phosphatidylethanolamine lipid bilayers
-
Suits, F.; Pitman, M. C.; Feller, S. E. Molecular dynamics investigation of the structural properties of phosphatidylethanolamine lipid bilayers J. Chem. Phys. 2005, 122, 244714
-
(2005)
J. Chem. Phys.
, vol.122
, pp. 244714
-
-
Suits, F.1
Pitman, M.C.2
Feller, S.E.3
-
11
-
-
24944443306
-
Effect of cholesterol on the properties of phospholipid membranes. 4. Interatomic voids
-
Alinchenko, M. G.; Voloshin, V. P.; Medvedev, N. N.; Mezei, M.; Pártay, L.; Jedlovszky, P. Effect of cholesterol on the properties of phospholipid membranes. 4. Interatomic voids J. Phys. Chem. B 2005, 109, 16490-16502
-
(2005)
J. Phys. Chem. B
, vol.109
, pp. 16490-16502
-
-
Alinchenko, M.G.1
Voloshin, V.P.2
Medvedev, N.N.3
Mezei, M.4
Pártay, L.5
Jedlovszky, P.6
-
12
-
-
0000059270
-
Martensitic Transition in a Confined Colloidal Suspension
-
Weiss, J. A.; Oxtoby, D. W.; Grier, D. G.; Murray, C. A. Martensitic Transition in a Confined Colloidal Suspension J. Chem. Phys. 1995, 103, 1180-1190
-
(1995)
J. Chem. Phys.
, vol.103
, pp. 1180-1190
-
-
Weiss, J.A.1
Oxtoby, D.W.2
Grier, D.G.3
Murray, C.A.4
-
13
-
-
83855161663
-
Analysis of lipid surface area in protein-membrane systems combining Voronoi tessellation and Monte Carlo integration methods
-
Mori, T.; Ogushi, F.; Sugita, Y. Analysis of lipid surface area in protein-membrane systems combining Voronoi tessellation and Monte Carlo integration methods J. Comput. Chem. 2012, 33, 286-293
-
(2012)
J. Comput. Chem.
, vol.33
, pp. 286-293
-
-
Mori, T.1
Ogushi, F.2
Sugita, Y.3
-
14
-
-
10844241458
-
Morphology of voids in molecular systems. A Voronoi-Delaunay analysis of a simulated DMPC membrane
-
Alinchenko, M. G.; Anikeenko, A.; Medvedev, N. N.; Voloshin, V. P.; Mezei, M.; Jedlovszky, P. Morphology of voids in molecular systems. A Voronoi-Delaunay analysis of a simulated DMPC membrane J. Phys. Chem. B 2004, 108, 19056-19067
-
(2004)
J. Phys. Chem. B
, vol.108
, pp. 19056-19067
-
-
Alinchenko, M.G.1
Anikeenko, A.2
Medvedev, N.N.3
Voloshin, V.P.4
Mezei, M.5
Jedlovszky, P.6
-
15
-
-
0030381077
-
The Quickhull Algorithm for Convex Hulls. ACM Trans
-
Barber, C. B.; Dobkin, D. P.; Huhdanpaa, H. The Quickhull Algorithm for Convex Hulls. ACM Trans Math. Softw. 1996, 22, 469-483
-
(1996)
Math. Softw.
, vol.22
, pp. 469-483
-
-
Barber, C.B.1
Dobkin, D.P.2
Huhdanpaa, H.3
-
16
-
-
84940605935
-
Triangle: Engineering a 2D Quality Mesh Generator and Delaunay Triangulator
-
Lin, M. C. Manocha, D. Springer-Verlag: New York
-
Shewchuk, J. R. Triangle: Engineering a 2D Quality Mesh Generator and Delaunay Triangulator. In Lecture Notes in Computer Science; Lin, M. C.; Manocha, D., Eds.; Springer-Verlag: New York, 1996; pp 203-222.
-
(1996)
Lecture Notes in Computer Science
, pp. 203-222
-
-
Shewchuk, J.R.1
-
17
-
-
84888628578
-
-
Geometric Dual Graph.
-
Weisstein, E. W. Geometric Dual Graph. http://mathworld.wolfram.com/ GeometricDualGraph.html.
-
-
-
Weisstein, E.W.1
-
18
-
-
84878586785
-
Definitions and Basic Properties of Voronoi Diagrams
-
John Wiley & Sons, Inc. Hoboken, NJ
-
Okabe, A.; Boots, B.; Sugihara, K.; Chiu, S. Definitions and Basic Properties of Voronoi Diagrams. In Spatial Tessellations: Concepts and Applications of Voronoi Diagrams; John Wiley & Sons, Inc.: Hoboken, NJ, 2008; pp 43-112.
-
(2008)
Spatial Tessellations: Concepts and Applications of Voronoi Diagrams
, pp. 43-112
-
-
Okabe, A.1
Boots, B.2
Sugihara, K.3
Chiu, S.4
-
19
-
-
23244434875
-
Response to comment by Almeida et al.: Free area theories for lipid bilayers-predictive or not?
-
Falck, E.; Patra, M.; Karttunen, M.; Hyvönen, M. T.; Vattulainen, I. Response to comment by Almeida et al.: free area theories for lipid bilayers-predictive or not? Biophys. J. 2005, 89, 745-752
-
(2005)
Biophys. J.
, vol.89
, pp. 745-752
-
-
Falck, E.1
Patra, M.2
Karttunen, M.3
Hyvönen, M.T.4
Vattulainen, I.5
-
20
-
-
58149204263
-
Ordering effects of cholesterol and its analogues
-
Róg, T.; Pasenkiewicz-Gierula, M.; Vattulainen, I.; Karttunen, M. Ordering effects of cholesterol and its analogues Biochim. Biophys. Acta, Rev. Biomembr. 2009, 1788, 97-121
-
(2009)
Biochim. Biophys. Acta, Rev. Biomembr.
, vol.1788
, pp. 97-121
-
-
Róg, T.1
Pasenkiewicz-Gierula, M.2
Vattulainen, I.3
Karttunen, M.4
-
21
-
-
24144488293
-
Areas of molecules in membranes consisting of mixtures
-
Edholm, O.; Nagle, J. F. Areas of molecules in membranes consisting of mixtures Biophys. J. 2005, 89, 1827-1832
-
(2005)
Biophys. J.
, vol.89
, pp. 1827-1832
-
-
Edholm, O.1
Nagle, J.F.2
-
22
-
-
0037381939
-
Molecular dynamics simulations of phospholipid bilayers with cholesterol
-
Hofsäss, C.; Lindahl, E.; Edholm, O. Molecular dynamics simulations of phospholipid bilayers with cholesterol Biophys. J. 2003, 84, 2192-2206
-
(2003)
Biophys. J.
, vol.84
, pp. 2192-2206
-
-
Hofsäss, C.1
Lindahl, E.2
Edholm, O.3
-
23
-
-
77953161754
-
A molecular view of the cholesterol condensing effect in DOPC lipid bilayers
-
Alwarawrah, M.; Dai, J.; Huang, J. A molecular view of the cholesterol condensing effect in DOPC lipid bilayers J. Phys. Chem. B 2010, 114, 7516-7523
-
(2010)
J. Phys. Chem. B
, vol.114
, pp. 7516-7523
-
-
Alwarawrah, M.1
Dai, J.2
Huang, J.3
-
24
-
-
4143120994
-
Sphingomyelin-Cholesterol Domains in Phospholipid Membranes: Atomistic Simulation
-
Pandit, S. A.; Vasudevan, S.; Chiu, S. W.; Mashl, R. J.; Jakobsson, E.; Scott, H. L. Sphingomyelin-Cholesterol Domains in Phospholipid Membranes: Atomistic Simulation Biophys. J. 2004, 87, 1092-1100
-
(2004)
Biophys. J.
, vol.87
, pp. 1092-1100
-
-
Pandit, S.A.1
Vasudevan, S.2
Chiu, S.W.3
Mashl, R.J.4
Jakobsson, E.5
Scott, H.L.6
-
25
-
-
0002196757
-
Polygons and Polyhedra
-
Heckbert, P. S. Morgan Kaufmann: Burlington, MA
-
Eric, H. Polygons and Polyhedra. In Graphics Gems IV; Heckbert, P. S., Ed.; Morgan Kaufmann: Burlington, MA, 1994; pp 24-47.
-
(1994)
Graphics Gems IV
, pp. 24-47
-
-
Eric, H.1
-
26
-
-
41149134824
-
Automated builder and database of protein/membrane complexes for molecular dynamics simulations
-
Jo, S.; Kim, T.; Im, W. Automated builder and database of protein/membrane complexes for molecular dynamics simulations PLoS One 2007, 2, 1-9
-
(2007)
PLoS One
, vol.2
, pp. 1-9
-
-
Jo, S.1
Kim, T.2
Im, W.3
-
27
-
-
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
-
28
-
-
65549083717
-
GridMAT-MD: A grid-based membrane analysis tool for use with molecular dynamics
-
Allen, W. J.; Lemkul, J. A.; Bevan, D. R. GridMAT-MD: a grid-based membrane analysis tool for use with molecular dynamics J. Comput. Chem. 2009, 30, 1952-1958
-
(2009)
J. Comput. Chem.
, vol.30
, pp. 1952-1958
-
-
Allen, W.J.1
Lemkul, J.A.2
Bevan, D.R.3
-
29
-
-
19744367689
-
Simulation of gel phase formation and melting in lipid bilayers using a coarse grained model
-
Marrink, S.-J.; Risselada, H. J.; Mark, A. E. Simulation of gel phase formation and melting in lipid bilayers using a coarse grained model Chem. Phys. Lipids 2005, 135, 223-244
-
(2005)
Chem. Phys. Lipids
, vol.135
, pp. 223-244
-
-
Marrink, S.-J.1
Risselada, H.J.2
Mark, A.E.3
-
30
-
-
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
-
31
-
-
77955657216
-
Structural implications of mutations assessed by molecular dynamics: Vpu1-32 from HIV-1
-
Krüger, J.; Fischer, W. B. Structural implications of mutations assessed by molecular dynamics: Vpu1-32 from HIV-1 Eur. Biophys. J. 2009, 39, 1069-1077
-
(2009)
Eur. Biophys. J.
, vol.39
, pp. 1069-1077
-
-
Krüger, J.1
Fischer, W.B.2
-
32
-
-
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
-
33
-
-
27344454932
-
GROMACS: Fast, flexible, and free
-
van der Spoel, D.; Lindahl, E.; Hess, B.; Groenhof, G.; Mark, A. E.; Berendsen, H. J. C. GROMACS: fast, flexible, and free J. Comput. Chem. 2005, 26, 1701-1718
-
(2005)
J. Comput. Chem.
, vol.26
, pp. 1701-1718
-
-
Van Der Spoel, D.1
Lindahl, E.2
Hess, B.3
Groenhof, G.4
Mark, A.E.5
Berendsen, H.J.C.6
-
34
-
-
0035789518
-
GROMACS 3.0: A package for molecular simulation and trajectory analysis
-
Lindahl, E.; Hess, B.; van der Spoel, D. GROMACS 3.0: a package for molecular simulation and trajectory analysis J. Mol. Model. 2001, 7, 306-317
-
(2001)
J. Mol. Model.
, vol.7
, pp. 306-317
-
-
Lindahl, E.1
Hess, B.2
Van Der Spoel, D.3
-
35
-
-
84942026338
-
Primitives for the manipulation of general subdivisions and the computation of Voronoi
-
Guibas, L.; Stolfi, J. Primitives for the manipulation of general subdivisions and the computation of Voronoi. ACM Trans. Graphics 1985, 4.
-
(1985)
ACM Trans. Graphics
, vol.4
-
-
Guibas, L.1
Stolfi, J.2
-
36
-
-
79960220458
-
CELLmicrocosmos 2.2 MembraneEditor: A Modular Interactive Shape- Based Software Approach to Solve Heterogeneous Membrane Packing Problems
-
Sommer, B.; Dingersen, T.; Gamroth, C.; Schneider, S. E.; Rubert, S.; Krüger, J.; Dietz, K.-J. CELLmicrocosmos 2.2 MembraneEditor: A Modular Interactive Shape- Based Software Approach To Solve Heterogeneous Membrane Packing Problems J. Chem. Inf. Model. 2011, 51, 1165-1182
-
(2011)
J. Chem. Inf. Model.
, vol.51
, pp. 1165-1182
-
-
Sommer, B.1
Dingersen, T.2
Gamroth, C.3
Schneider, S.E.4
Rubert, S.5
Krüger, J.6
Dietz, K.-J.7
-
37
-
-
34547474332
-
The MARTINI Force Field: Coarse Grained Model for Biomolecular Simulations
-
Marrink, S.-J.; Risselada, H. J.; Yefimov, S.; Tieleman, D. P.; de Vries, A. H. The MARTINI Force Field: Coarse Grained Model for Biomolecular Simulations J. Phys. Chem. B 2007, 111, 7812-7824
-
(2007)
J. Phys. Chem. B
, vol.111
, pp. 7812-7824
-
-
Marrink, S.-J.1
Risselada, H.J.2
Yefimov, S.3
Tieleman, D.P.4
De Vries, A.H.5
-
38
-
-
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. 1983, 81, 3684-3684
-
(1983)
J. Chem. Phys.
, vol.81
, pp. 3684-3684
-
-
Berendsen, H.J.C.1
Postma, J.P.M.2
Van Gunsteren, W.F.3
Dinola, A.4
Haak, J.R.5
-
39
-
-
0034634708
-
Structure of lipid bilayers
-
Tristram-Nagle, S.; Nagle, J. F.; Tristram-Nagle, S. Structure of lipid bilayers Biochim. Biophys. Acta, Rev. Biomembr. 2000, 1469, 159-37
-
(2000)
Biochim. Biophys. Acta, Rev. Biomembr.
, vol.1469
, pp. 159-237
-
-
Tristram-Nagle, S.1
Nagle, J.F.2
Tristram-Nagle, S.3
-
41
-
-
0037569250
-
A consistent potential energy parameter set for lipids: Dipalmitoylphosphatidylcholine as a benchmark of the GROMOS96 45A3 force field
-
Chandrasekhar, I.; Kastenholz, M.; Lins, R. D.; Oostenbrink, C.; Schuler, L. D.; Tieleman, D. P.; van Gunsteren, W. F. A consistent potential energy parameter set for lipids: dipalmitoylphosphatidylcholine as a benchmark of the GROMOS96 45A3 force field Eur. Biophys. J. 2003, 32, 67-77
-
(2003)
Eur. Biophys. J.
, vol.32
, pp. 67-77
-
-
Chandrasekhar, I.1
Kastenholz, M.2
Lins, R.D.3
Oostenbrink, C.4
Schuler, L.D.5
Tieleman, D.P.6
Van Gunsteren, W.F.7
-
42
-
-
35748967575
-
Acyl chain order parameter profiles in phospholipid bilayers: Computation from molecular dynamics simulations and comparison with 2H NMR experiments
-
Vermeer, L. S.; de Groot, B. L.; Réat, V.; Milon, A.; Czaplicki, J. Acyl chain order parameter profiles in phospholipid bilayers: computation from molecular dynamics simulations and comparison with 2H NMR experiments Eur. Biophys. J. 2007, 36, 919-931
-
(2007)
Eur. Biophys. J.
, vol.36
, pp. 919-931
-
-
Vermeer, L.S.1
De Groot, B.L.2
Réat, V.3
Milon, A.4
Czaplicki, J.5
-
43
-
-
0035854701
-
Visualizing detergent resistant domains in model membranes with atomic force microscopy
-
Rinia, H. A.; Snel, M. M.; van der Eerden, J. P.; de Kruijff, B. Visualizing detergent resistant domains in model membranes with atomic force microscopy FEBS Lett. 2001, 501, 92-96
-
(2001)
FEBS Lett.
, vol.501
, pp. 92-96
-
-
Rinia, H.A.1
Snel, M.M.2
Van Der Eerden, J.P.3
De Kruijff, B.4
-
44
-
-
33646446451
-
Structure of fully hydrated fluid phase lipid bilayers with monounsaturated chains
-
Kučerka, N.; Tristram-Nagle, S.; Nagle, J. F. Structure of fully hydrated fluid phase lipid bilayers with monounsaturated chains J. Membr. Biol. 2005, 208, 193-202
-
(2005)
J. Membr. Biol.
, vol.208
, pp. 193-202
-
-
Kučerka, N.1
Tristram-Nagle, S.2
Nagle, J.F.3
-
45
-
-
77957936649
-
Simulating POPC and POPC/POPG Bilayers: Conserved Packing and Altered Surface Reactivity
-
Janosi, L.; Gorfe, A. A. Simulating POPC and POPC/POPG Bilayers: Conserved Packing and Altered Surface Reactivity J. Chem. Theory Comput. 2010, 6, 3267-3273
-
(2010)
J. Chem. Theory Comput.
, vol.6
, pp. 3267-3273
-
-
Janosi, L.1
Gorfe, A.A.2
-
46
-
-
0025017861
-
Organization and interaction of cholesterol and phosphatidylcholine in model bilayer membranes
-
Hyslop, P. A.; Morel, B.; Sauerheber, R. D. Organization and interaction of cholesterol and phosphatidylcholine in model bilayer membranes Biochemistry 1990, 29, 1025-1038
-
(1990)
Biochemistry
, vol.29
, pp. 1025-1038
-
-
Hyslop, P.A.1
Morel, B.2
Sauerheber, R.D.3
-
47
-
-
0030876951
-
Phosphatidylcholine acyl unsaturation modulates the decrease in interfacial elasticity induced by cholesterol
-
Smaby, J. M.; Momsen, M. M.; Brockman, H. L.; Brown, R. E. Phosphatidylcholine acyl unsaturation modulates the decrease in interfacial elasticity induced by cholesterol Biophys. J. 1997, 73, 1492-1505
-
(1997)
Biophys. J.
, vol.73
, pp. 1492-1505
-
-
Smaby, J.M.1
Momsen, M.M.2
Brockman, H.L.3
Brown, R.E.4
|