-
1
-
-
0017776823
-
Dynamics of folded proteins
-
McCammon, J.A.; Gelin, B.R.; Karplus, M. Dynamics of folded proteins. Nature 1977, 267, 585-590.
-
(1977)
Nature
, vol.267
, pp. 585-590
-
-
Mccammon, J.A.1
Gelin, B.R.2
Karplus, M.3
-
2
-
-
72049092011
-
Membrane-bending mechanism of amphiphysin N-BAR domains
-
Arkhipov, A.; Yin, Y.; Schulten, K. Membrane-bending mechanism of amphiphysin N-BAR domains. Biophys. J. 2009, 97, 2727-2735.
-
(2009)
Biophys. J.
, vol.97
, pp. 2727-2735
-
-
Arkhipov, A.1
Yin, Y.2
Schulten, K.3
-
3
-
-
43149103416
-
Mechanosensitive membrane channels in action
-
Yefimov, S.; van der Giessen, E.; Onck, P.R.; Marrink, S.J. Mechanosensitive membrane channels in action. Biophys. J. 2008, 94, 2994-3002.
-
(2008)
Biophys. J.
, vol.94
, pp. 2994-3002
-
-
Yefimov, S.1
Van der Giessen, E.2
Onck, P.R.3
Marrink, S.J.4
-
4
-
-
77954912142
-
Immobilization of the plug domain inside the SecY channel allows unrestricted protein translocation
-
A Nijeholt, J.A.L.; Bulacu, M.; Marrink, S.J.; Driessen, A.J.M. Immobilization of the plug domain inside the SecY channel allows unrestricted protein translocation. J. Biol. Chem. 2010, 285, 23747-23754.
-
(2010)
J. Biol. Chem.
, vol.285
, pp. 23747-23754
-
-
Nijeholt, J.A.L.A.1
Bulacu, M.2
Marrink, S.J.3
Driessen, A.J.M.4
-
5
-
-
33847258823
-
Bilayer deformation by the Kv channel voltage sensor domain revealed by self-assembly simulations
-
Bond, P.J.; Sansom, M.S.P. Bilayer deformation by the Kv channel voltage sensor domain revealed by self-assembly simulations. Proc. Natl. Acad. Sci. USA 2007, 104, 2631-2636.
-
(2007)
Proc. Natl. Acad. Sci. USA
, vol.104
, pp. 2631-2636
-
-
Bond, P.J.1
Sansom, M.S.P.2
-
6
-
-
33847193915
-
Assembly of lipoprotein particles revealed by coarse-grained molecular dynamics simulations
-
Shih, A.Y.; Freddolino, P.L.; Arkhipov, A.; Schulten, K. Assembly of lipoprotein particles revealed by coarse-grained molecular dynamics simulations. J. Struct. Biol. 2007, 157, 579-592.
-
(2007)
J. Struct. Biol.
, vol.157
, pp. 579-592
-
-
Shih, A.Y.1
Freddolino, P.L.2
Arkhipov, A.3
Schulten, K.4
-
7
-
-
58149314529
-
Probing peptide nanotube self-assembly at a liquid-liquid interface with coarse-grained molecular dynamics
-
Khurana, E.; DeVane, R.H.; Kohlmeyer, A.; Klein, M.L. Probing peptide nanotube self-assembly at a liquid-liquid interface with coarse-grained molecular dynamics. Nano Lett. 2008, 8, 3626-3630.
-
(2008)
Nano Lett.
, vol.8
, pp. 3626-3630
-
-
Khurana, E.1
Devane, R.H.2
Kohlmeyer, A.3
Klein, M.L.4
-
8
-
-
77957901688
-
Lipid-mediated interactions tune the association of glycophorin A helix and its disruptive mutants in membranes
-
Sengupta, D.; Marrink, S.J. Lipid-mediated interactions tune the association of glycophorin A helix and its disruptive mutants in membranes. Phys. Chem. Chem. Phys. 2010, 12, 12987-12996.
-
(2010)
Phys. Chem. Chem. Phys.
, vol.12
, pp. 12987-12996
-
-
Sengupta, D.1
Marrink, S.J.2
-
9
-
-
79955648135
-
Determining peptide partitioning properties via computer simulation
-
Ulmschneider, J.P.; Andersson, M.; Ulmschneider, M.B. Determining peptide partitioning properties via computer simulation. J. Membr. Biol. 2011, 239, 15-26.
-
(2011)
J. Membr. Biol.
, vol.239
, pp. 15-26
-
-
Ulmschneider, J.P.1
Andersson, M.2
Ulmschneider, M.B.3
-
10
-
-
67649989357
-
A single bicontinuous cubic phase induced by fusion peptides
-
Fuhrmans, M.; Knecht, V.; Marrink, S.J. A single bicontinuous cubic phase induced by fusion peptides. J. Am. Chem. Soc. 2009, 131, 9166-9167.
-
(2009)
J. Am. Chem. Soc.
, vol.131
, pp. 9166-9167
-
-
Fuhrmans, M.1
Knecht, V.2
Marrink, S.J.3
-
11
-
-
77958483330
-
Direct simulation of protein-mediated vesicle fusion: Lung surfactant protein B
-
Baoukina, S.; Tieleman, D.P. Direct simulation of protein-mediated vesicle fusion: Lung surfactant protein B. Biophys. J. 2010, 99, 2134-2142.
-
(2010)
Biophys. J.
, vol.99
, pp. 2134-2142
-
-
Baoukina, S.1
Tieleman, D.P.2
-
12
-
-
84934444294
-
Vesicles and Vesicle Fusion: Coarse-Grained Simulations
-
Humana Press: New York, NY, USA
-
Shillcock, J. Vesicles and Vesicle Fusion: Coarse-Grained Simulations. In Methods in Molecular Biology; Monticelli, L., Salonen, E., Eds.; Humana Press: New York, NY, USA, 2013; Volume 924, pp. 659-697.
-
(2013)
In Methods in Molecular Biology; Monticelli, L., Salonen, E., Eds.
, vol.924
, pp. 659-697
-
-
Shillcock, J.1
-
13
-
-
53249119350
-
Helix-helix interactions in membrane proteins: Coarse-grained simulations of glycophorin a helix dimerization
-
Psachoulia, E.; Fowler, P.W.; Bond, P.J.; Sansom, M.S.P. Helix-helix interactions in membrane proteins: Coarse-grained simulations of glycophorin a helix dimerization. Biochemistry 2008, 47, 10503-10512.
-
(2008)
Biochemistry
, vol.47
, pp. 10503-10512
-
-
Psachoulia, E.1
Fowler, P.W.2
Bond, P.J.3
Sansom, M.S.P.4
-
14
-
-
70149098505
-
Coarse-grained modeling of allosteric regulation in protein receptors
-
Balabin, I.A.; Yang, W.; Beratan, D.N. Coarse-grained modeling of allosteric regulation in protein receptors. Proc. Natl. Acad. Sci. USA 2009, 106, 14253-14258.
-
(2009)
Proc. Natl. Acad. Sci. USA
, vol.106
, pp. 14253-14258
-
-
Balabin, I.A.1
Yang, W.2
Beratan, D.N.3
-
15
-
-
77953377650
-
Update of the CHARMM all-atom additive force field for lipids: Validation on six lipid types
-
Klauda, J.B.; Venable, R.M.; Freites, J.A.; O'Connor, J.W.; Tobias, D.J.; Mondragon-Ramirez, C.; Vorobyov, I.; MacKerell, A.D.; Pastor, R.W. Update of the CHARMM all-atom additive force field for lipids: Validation on six lipid types. J. Phys. Chem. B 2010, 114, 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, A.D.8
Pastor, R.W.9
-
16
-
-
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
-
17
-
-
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
-
18
-
-
64649101249
-
Long-timescale molecular dynamics simulations of protein structure and function
-
Klepeis, J.L.; Lindorff-Larsen, K.; Dror, R.O.; Shaw, D.E. Long-timescale molecular dynamics simulations of protein structure and function. Curr. Opin. Struct. Biol. 2009, 19, 120-127.
-
(2009)
Curr. Opin. Struct. Biol.
, vol.19
, pp. 120-127
-
-
Klepeis, J.L.1
Lindorff-Larsen, K.2
Dror, R.O.3
Shaw, D.E.4
-
19
-
-
64649105762
-
Accelerating molecular dynamic simulation on graphics processing units
-
Friedrichs, M.S.; Eastman, P.; Vaidyanathan, V.; Houston, M.; Legrand, S.; Beberg, A.L.; Ensign, D.L.; Bruns, C.M.; Pande, V.S. Accelerating molecular dynamic simulation on graphics processing units. J. Comput. Chem. 2009, 30, 864-872.
-
(2009)
J. Comput. Chem.
, vol.30
, pp. 864-872
-
-
Friedrichs, M.S.1
Eastman, P.2
Vaidyanathan, V.3
Houston, M.4
Legrand, S.5
Beberg, A.L.6
Ensign, D.L.7
Bruns, C.M.8
Pande, V.S.9
-
20
-
-
77957572546
-
Challenges in protein-folding simulations
-
Freddolino, P.L.; Harrison, C.B.; Liu, Y.; Schulten, K. Challenges in protein-folding simulations. Nat. Phys. 2010, 6, 751-758.
-
(2010)
Nat. Phys.
, vol.6
, pp. 751-758
-
-
Freddolino, P.L.1
Harrison, C.B.2
Liu, Y.3
Schulten, K.4
-
21
-
-
77955729387
-
The multiscale coarse-graining method: Assessing its accuracy and introducing density dependent coarse-grain potentials
-
064109:1-064109:16
-
Izvekov, S.; Chung, P.W.; Rice, B.M. The multiscale coarse-graining method: Assessing its accuracy and introducing density dependent coarse-grain potentials. J. Chem. Phys. 2010, 133, 064109:1-064109:16.
-
(2010)
J. Chem. Phys.
, vol.133
-
-
Izvekov, S.1
Chung, P.W.2
Rice, B.M.3
-
22
-
-
80054706972
-
Exploration of transferability in multiscale coarse-grained peptide models
-
Thorpe, I.F.; Goldenberg, D.P.; Voth, G.A. Exploration of transferability in multiscale coarse-grained peptide models. J. Phys. Chem. B 2011, 115, 11911-11926.
-
(2011)
J. Phys. Chem. B
, vol.115
, pp. 11911-11926
-
-
Thorpe, I.F.1
Goldenberg, D.P.2
Voth, G.A.3
-
23
-
-
80051740011
-
A challenge for peptide coarse graining: Transferability of fragment-based models
-
Engin, O.; Villa, A.; Peter, C.; Sayar, M. A challenge for peptide coarse graining: Transferability of fragment-based models. Macromol. Theory Simul. 2011, 20, 451-465.
-
(2011)
Macromol. Theory Simul.
, vol.20
, pp. 451-465
-
-
Engin, O.1
Villa, A.2
Peter, C.3
Sayar, M.4
-
24
-
-
84883303199
-
Challenges in multiscale modeling of polymer dynamics
-
Li, Y.; Abberton, B.C.; Kroger, M.; Liu, W.K. Challenges in multiscale modeling of polymer dynamics. Polymers 2013, 5, 751-832.
-
(2013)
Polymers
, vol.5
, pp. 751-832
-
-
Li, Y.1
Abberton, B.C.2
Kroger, M.3
Liu, W.K.4
-
25
-
-
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
-
26
-
-
27344436659
-
Scalable molecular dynamics with NAMD
-
Phillips, J.C.; Braun, R.; Wang, W.; Gumbart, J.; Tajkhorshid, E.; Villa, E.; Chipot, C.; Skeel, R.D.; Kalé, L.; Schulten, K. Scalable molecular dynamics with NAMD. J. Comput. Chem. 2005, 26, 1781-1802.
-
(2005)
J. Comput. Chem.
, vol.26
, pp. 1781-1802
-
-
Phillips, J.C.1
Braun, R.2
Wang, W.3
Gumbart, J.4
Tajkhorshid, E.5
Villa, E.6
Chipot, C.7
Skeel, R.D.8
Kalé, L.9
Schulten, K.10
-
27
-
-
2942532422
-
Development and testing of a general amber force field
-
Wang, J.; Wolf, R.M.; Caldwell, J.W.; Kollman, P.A.; Case, D.A. Development and testing of a general amber force field. J. Comput. Chem. 2004, 25, 1157-1174.
-
(2004)
J. Comput. Chem.
, vol.25
, pp. 1157-1174
-
-
Wang, J.1
Wolf, R.M.2
Caldwell, J.W.3
Kollman, P.A.4
Case, D.A.5
-
28
-
-
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
-
29
-
-
0038418623
-
Coarse-grained models and collective phenomena in membranes: Computer simulation of membrane fusion
-
Müller, M.; Katsov, K.; Schick, M. Coarse-grained models and collective phenomena in membranes: Computer simulation of membrane fusion. J. Polym. Sci. B Polym. Phys. 2003, 41, 1441-1450.
-
(2003)
J. Polym. Sci. B Polym. Phys.
, vol.41
, pp. 1441-1450
-
-
Müller, M.1
Katsov, K.2
Schick, M.3
-
31
-
-
36549097755
-
Monte Carlo lattice simulation of amphiphilic systems in two and three dimensions
-
Larson, R. Monte Carlo lattice simulation of amphiphilic systems in two and three dimensions. J. Chem. Phys. 1988, 89, 1642-1650.
-
(1988)
J. Chem. Phys.
, vol.89
, pp. 1642-1650
-
-
Larson, R.1
-
32
-
-
0000862725
-
Computer simulations of a water/oil interface in the presence of micelles
-
Smit, B.; Hilbers, P.A.J.; Esselink, K.; Rupert, L.A.M.; van Os, N.M.; Schlijper, A.G. Computer simulations of a water/oil interface in the presence of micelles. Nature 1990, 348, 624-625.
-
(1990)
Nature
, vol.348
, pp. 624-625
-
-
Smit, B.1
Hilbers, P.A.J.2
Esselink, K.3
Rupert, L.A.M.4
Van Os, N.M.5
Schlijper, A.G.6
-
33
-
-
0000206982
-
Computer simulations of bilayer membranes: Self-assembly and interfacial tension
-
Goetz, R.; Lipowsky, R. Computer simulations of bilayer membranes: Self-assembly and interfacial tension. J. Chem. Phys. 1998, 108, 7397-7409.
-
(1998)
J. Chem. Phys.
, vol.108
, pp. 7397-7409
-
-
Goetz, R.1
Lipowsky, R.2
-
34
-
-
0000283071
-
Mobility and elasticity of self-assembled membranes
-
Goetz, R.; Gompper, G.; Lipowsky, R. Mobility and elasticity of self-assembled membranes. Phys. Rev. Lett. 1999, 82, 221-224.
-
(1999)
Phys. Rev. Lett.
, vol.82
, pp. 221-224
-
-
Goetz, R.1
Gompper, G.2
Lipowsky, R.3
-
35
-
-
84950109965
-
Simulating microscopic hydrodynamic phenomena with dissipative particle dynamics
-
doi:101209/0295-5075/19/3/001
-
Hoogerbrugge, P.J.; Koelman, J.M.V.A. Simulating microscopic hydrodynamic phenomena with dissipative particle dynamics. Europhys. Lett. 1992, 19, doi:10.1209/0295-5075/19/3/001.
-
(1992)
Europhys. Lett.
, vol.19
-
-
Hoogerbrugge, P.J.1
Koelman, J.M.V.A.2
-
36
-
-
84956259119
-
Statistical mechanics of dissipative particle dynamics
-
doi:101209/0295-5075/30/4/001
-
Español, P.; Warren, P. Statistical mechanics of dissipative particle dynamics. Europhys. Lett. 1995, 30, doi:10.1209/0295-5075/30/4/001.
-
(1995)
Europhys. Lett.
, vol.30
-
-
Español, P.1
Warren, P.2
-
37
-
-
5544242655
-
Dissipative particle dynamics: Bridging the gap between atomistic and mesoscopic simulation
-
Groot, R.D.;Warren, P.B. Dissipative particle dynamics: Bridging the gap between atomistic and mesoscopic simulation. J. Chem. Phys. 1997, 107, 4423-4435.
-
(1997)
J. Chem. Phys.
, vol.107
, pp. 4423-4435
-
-
Groot, R.D.1
Arren, P.B.2
-
38
-
-
16244363029
-
Simulating the self-assembly of model membranes
-
Venturoli, M.; Smit, B. Simulating the self-assembly of model membranes. PhysChemComm 1999, 2, 45-49.
-
(1999)
PhysChemComm
, vol.2
, pp. 45-49
-
-
Venturoli, M.1
Smit, B.2
-
39
-
-
34547287578
-
Pathway of membrane fusion with two tension-dependent energy barriers
-
218101:1-218101:4
-
Grafmüller, A.; Shillcock, J.; Lipowsky, R. Pathway of membrane fusion with two tension-dependent energy barriers. Phys. Rev. Lett. 2007, 98, 218101:1-218101:4.
-
(2007)
Phys. Rev. Lett.
, vol.98
-
-
Grafmüller, A.1
Shillcock, J.2
Lipowsky, R.3
-
40
-
-
21244431672
-
Simulation studies of protein-induced bilayer deformations, and lipid-induced protein tilting, on a mesoscopic model for lipid bilayers with embedded proteins
-
Venturoli, M. Simulation studies of protein-induced bilayer deformations, and lipid-induced protein tilting, on a mesoscopic model for lipid bilayers with embedded proteins. Biophys. J. 2005, 88, 1778-1798.
-
(2005)
Biophys. J.
, vol.88
, pp. 1778-1798
-
-
Venturoli, M.1
-
41
-
-
0034909360
-
Mesoscopic simulation of cell membrane damage, morphology change and rupture by nonionic surfactants
-
Groot, R.; Rabone, K. Mesoscopic simulation of cell membrane damage, morphology change and rupture by nonionic surfactants. Biophys. J. 2001, 81, 725-736.
-
(2001)
Biophys. J.
, vol.81
, pp. 725-736
-
-
Groot, R.1
Rabone, K.2
-
42
-
-
33750980984
-
Mesoscopic models of biological membranes
-
Venturoli, M.; Maddalena Sperotto, M.; Kranenburg, M.; Smit, B. Mesoscopic models of biological membranes. Phys. Rep. 2006, 437, 1-54.
-
(2006)
Phys. Rep.
, vol.437
, pp. 1-54
-
-
Venturoli, M.1
Maddalena Sperotto, M.2
Kranenburg, M.3
Smit, B.4
-
43
-
-
84867341613
-
Efficient algorithms for langevin and DPD dynamics
-
Goga, N.; Rzepiela, A.J.; de Vries, A.H.; Marrink, S.J.; Berendsen, H.J.C. Efficient algorithms for langevin and DPD dynamics. J. Chem. Theory Comput. 2012, 8, 3637-3649.
-
(2012)
J. Chem. Theory Comput.
, vol.8
, pp. 3637-3649
-
-
Goga, N.1
Rzepiela, A.J.2
De Vries, A.H.3
Marrink, S.J.4
Berendsen, H.J.C.5
-
44
-
-
0035902367
-
A coarse grain model for phospholipid simulations
-
Shelley, J.C.; Shelley, M.Y.; Reeder, R.C.; Bandyopadhyay, S.; Klein, M.L. A coarse grain model for phospholipid simulations. J. Phys. Chem. B 2001, 105, 4464-4470.
-
(2001)
J. Phys. Chem. B
, vol.105
, pp. 4464-4470
-
-
Shelley, J.C.1
Shelley, M.Y.2
Reeder, R.C.3
Bandyopadhyay, S.4
Klein, M.L.5
-
45
-
-
0034250744
-
An improved empirical potential energy function for molecular simulations of phospholipids
-
Feller, S.E.; MacKerell, A.D. An improved empirical potential energy function for molecular simulations of phospholipids. J. Phys. Chem. B 2000, 104, 7510-7515.
-
(2000)
J. Phys. Chem. B
, vol.104
, pp. 7510-7515
-
-
Feller, S.E.1
Mackerell, A.D.2
-
46
-
-
36248975150
-
-
Available online: (accessed on 28 June 2013)
-
Van der Spoel, D.; Lindahl, E.; Hess, B.; van Buuren, A.; Apol, E.; Meulenhoff, P.; Tieleman, D.; Sijbers, A.; Feenstra, K.; van Drunen, R.; et al. Gromacs User Manual version 4.0. Available online: http://www.gromacs.org/ (accessed on 28 June 2013).
-
Gromacs User Manual version 4.0.
-
-
Van der Spoel, D.1
Lindahl, E.2
Hess, B.3
Van Buuren, A.4
Apol, E.5
Meulenhoff, P.6
Tieleman, D.7
Sijbers, A.8
Feenstra, K.9
Van Drunen, R.10
-
47
-
-
33645078713
-
Calculation of effective interaction potentials from radial distribution functions: A reverse Monte Carlo approach
-
Lyubartsev, A.P.; Laaksonen, A. Calculation of effective interaction potentials from radial distribution functions: A reverse Monte Carlo approach. Phys. Rev. E 1995, 52, 3730-3737.
-
(1995)
Phys. Rev. E
, vol.52
, pp. 3730-3737
-
-
Lyubartsev, A.P.1
Laaksonen, A.2
-
48
-
-
0027693073
-
Estimation of interfacial tension between organic liquids and water
-
Demond, A.H.; Lindner, A.S. Estimation of interfacial tension between organic liquids and water. Environ. Sci. Technol. 1993, 27, 2318-2331.
-
(1993)
Environ. Sci. Technol.
, vol.27
, pp. 2318-2331
-
-
Demond, A.H.1
Lindner, A.S.2
-
49
-
-
14544291957
-
A multiscale coarse-graining method for biomolecular systems
-
Izvekov, S.; Voth, G.A. A multiscale coarse-graining method for biomolecular systems. J. Phys. Chem. B 2005, 109, 2469-2473.
-
(2005)
J. Phys. Chem. B
, vol.109
, pp. 2469-2473
-
-
Izvekov, S.1
Voth, G.A.2
-
50
-
-
3042598406
-
Effective force fields for condensed phase systems from ab initio molecular dynamics simulation: A new method for force-matching
-
10896:1-10896:18
-
Izvekov, S.; Parrinello, M., Burnham, C.J.; Voth, G.A. Effective force fields for condensed phase systems from ab initio molecular dynamics simulation: A new method for force-matching. J. Chem. Phys. 2004, 120, 10896:1-10896:18.
-
(2004)
J. Chem. Phys.
, vol.120
-
-
Izvekov, S.1
Parrinello, M.2
Burnham, C.J.3
Voth, G.A.4
-
51
-
-
25444487536
-
Systematic coarse-graining of nanoparticle interactions in molecular dynamics simulation
-
Izvekov, S.; Violi, A.; Voth, G.A. Systematic coarse-graining of nanoparticle interactions in molecular dynamics simulation. J. Phys. Chem. B 2005, 109, 17019-17024.
-
(2005)
J. Phys. Chem. B
, vol.109
, pp. 17019-17024
-
-
Izvekov, S.1
Violi, A.2
Voth, G.A.3
-
52
-
-
84940492598
-
Interatomic potentials from first-principles calculations: The force-matching method
-
doi:101209/0295-5075/26/8/005
-
Ercolessi, F.; Adams, J.B. Interatomic potentials from first-principles calculations: The force-matching method. Europhys. Lett. 1994, 26, 583, doi:10.1209/0295-5075/26/8/005.
-
(1994)
Europhys. Lett.
, vol.26
, pp. 583
-
-
Ercolessi, F.1
Adams, J.B.2
-
54
-
-
38949097417
-
A quantitative coarse-grain model for lipid bilayers
-
Orsi, M.; Haubertin, D.Y.; Sanderson, W.E.; Essex, J.W. A quantitative coarse-grain model for lipid bilayers. J. Phys. Chem. B 2008, 112, 802-815.
-
(2008)
J. Phys. Chem. B
, vol.112
, pp. 802-815
-
-
Orsi, M.1
Haubertin, D.Y.2
Sanderson, W.E.3
Essex, J.W.4
-
55
-
-
64749105956
-
Hybrid coarse-graining approach for lipid bilayers at large length and time scales
-
Ayton, G.S.; Voth, G.A. Hybrid coarse-graining approach for lipid bilayers at large length and time scales. J. Phys. Chem. B 2009, 113, 4413-4424.
-
(2009)
J. Phys. Chem. B
, vol.113
, pp. 4413-4424
-
-
Ayton, G.S.1
Voth, G.A.2
-
56
-
-
70350233625
-
Hierarchical coarse-graining strategy for protein-membrane systems to access mesoscopic scales
-
Ayton, G.S.; Lyman, E.; Voth, G.A. Hierarchical coarse-graining strategy for protein-membrane systems to access mesoscopic scales. Faraday Discuss. 2010, 144, 347-357.
-
(2010)
Faraday Discuss.
, vol.144
, pp. 347-357
-
-
Ayton, G.S.1
Lyman, E.2
Voth, G.A.3
-
57
-
-
0001283690
-
The structure of a highly concentrated aqueous solution of lithium chloride
-
doi:101088/0022- 3719/18/22/005
-
Copestake, A.P.; Neilson, G.W.; Enderby, J.E. The structure of a highly concentrated aqueous solution of lithium chloride. J. Phys. C Solid State Phys. 1985, 18, doi:10.1088/0022- 3719/18/22/005.
-
(1985)
J. Phys. C Solid State Phys.
, vol.18
-
-
Copestake, A.P.1
Neilson, G.W.2
Enderby, J.E.3
-
59
-
-
30444448249
-
The GROMOS software for biomolecular simulation: GROMOS05
-
Christen, M.; Hünenberger, P.H.; Bakowies, D.; Baron, R.; Bürgi, R.; Geerke, D.P.; Heinz, T.N.; Kastenholz, M.A.; Kräutler, V.; Oostenbrink, C.; et al. The GROMOS software for biomolecular simulation: GROMOS05. J. Comput. Chem. 2005, 26, 1719-1751.
-
(2005)
J. Comput. Chem.
, vol.26
, pp. 1719-1751
-
-
Christen, M.1
Hünenberger, P.H.2
Bakowies, D.3
Baron, R.4
Bürgi, R.5
Geerke, D.P.6
Heinz, T.N.7
Kastenholz, M.A.8
Kräutler, V.9
Oostenbrink, C.10
-
60
-
-
1642485164
-
Coarse grained model for semiquantitative lipid simulations
-
Marrink, S.J.; de Vries, A.H.; Mark, A.E. Coarse grained model for semiquantitative lipid simulations. J. Phys. Chem. B 2004, 108, 750-760.
-
(2004)
J. Phys. Chem. B
, vol.108
, pp. 750-760
-
-
Marrink, S.J.1
De Vries, A.H.2
Mark, A.E.3
-
61
-
-
33646523709
-
Solubilities of water in several normal alkanes from C7 to C161
-
Schatzberg, P. Solubilities of water in several normal alkanes from C7 to C161. J. Phys. Chem. 1963, 67, 776-779.
-
(1963)
J. Phys. Chem.
, vol.67
, pp. 776-779
-
-
Schatzberg, P.1
-
62
-
-
0000433140
-
Prediction of solvation free energies of small organic molecules additive-constitutive models based on molecular fingerprints and atomic constants
-
Viswanadhan, V.N.; Ghose, A.K.; Singh, U.C.; Wendoloski, J.J. Prediction of solvation free energies of small organic molecules additive-constitutive models based on molecular fingerprints and atomic constants. J. Chem. Inf. Comput. Sci. 1999, 39, 405-412.
-
(1999)
J. Chem. Inf. Comput. Sci.
, vol.39
, pp. 405-412
-
-
Viswanadhan, V.N.1
Ghose, A.K.2
Singh, U.C.3
Wendoloski, J.J.4
-
63
-
-
0034728673
-
Prediction of properties from simulations: Free energies of solvation in hexadecane, octanol, and water
-
Duffy, E.M.; Jorgensen, W.L. Prediction of properties from simulations: Free energies of solvation in hexadecane, octanol, and water. J. Am. Chem. Soc. 2000, 122, 2878-2888.
-
(2000)
J. Am. Chem. Soc.
, vol.122
, pp. 2878-2888
-
-
Duffy, E.M.1
Jorgensen, W.L.2
-
64
-
-
33646744629
-
Diffusion in paraffin hydrocarbons
-
Douglass, D.C.; McCall, D.W. Diffusion in paraffin hydrocarbons. J. Phys. Chem. 1958, 62, 1102-1107.
-
(1958)
J. Phys. Chem.
, vol.62
, pp. 1102-1107
-
-
Douglass, D.C.1
Mccall, D.W.2
-
65
-
-
37049095962
-
Pressure and temperature dependence of self-diffusion in water
-
Krynicki, K.; Green, C.D.; Sawyer, D.W. Pressure and temperature dependence of self-diffusion in water. Faraday Discuss. Chem. Soc. 1978, 66, 199-208.
-
(1978)
Faraday Discuss. Chem. Soc.
, vol.66
, pp. 199-208
-
-
Krynicki, K.1
Green, C.D.2
Sawyer, D.W.3
-
66
-
-
33847316387
-
Comparison of thermodynamic properties of coarse-grained and atomic-level simulation models
-
Baron, R.; Trzesniak, D.; de Vries, A.H.; Elsener, A.; Marrink, S.J.; van Gunsteren, W.F. Comparison of thermodynamic properties of coarse-grained and atomic-level simulation models. ChemPhysChem 2007, 8, 452-461.
-
(2007)
ChemPhysChem
, vol.8
, pp. 452-461
-
-
Baron, R.1
Trzesniak, D.2
De Vries, A.H.3
Elsener, A.4
Marrink, S.J.5
Van Gunsteren, W.F.6
-
67
-
-
0036250448
-
Dynamic interfacial tension behavior of water/oil systems containing in situ-formed surfactants
-
Amaya, J.; Rana, D.; Hornof, V. Dynamic interfacial tension behavior of water/oil systems containing in situ-formed surfactants. J. Solut. Chem. 2002, 31, 139-148.
-
(2002)
J. Solut. Chem.
, vol.31
, pp. 139-148
-
-
Amaya, J.1
Rana, D.2
Hornof, V.3
-
69
-
-
77952710577
-
Zwitterionic lipid assemblies: Molecular dynamics studies of monolayers, bilayers, and vesicles using a new coarse grain force field
-
Shinoda,W.; DeVane, R.; Klein, M.L. Zwitterionic lipid assemblies: Molecular dynamics studies of monolayers, bilayers, and vesicles using a new coarse grain force field. J. Phys. Chem. B 2010, 114, 6836-6849.
-
(2010)
J. Phys. Chem. B
, vol.114
, pp. 6836-6849
-
-
Shinoda, W.1
Devane, R.2
Klein, M.L.3
-
71
-
-
0032562213
-
Thermodynamics of membrane partitioning for a series of n-alcohols determined by titration calorimetry: Role of hydrophobic effects
-
Rowe, E.S.; Zhang, F.; Leung, T.W.; Parr, J.S.; Guy, P.T. Thermodynamics of membrane partitioning for a series of n-alcohols determined by titration calorimetry: Role of hydrophobic effects. Biochemistry 1998, 37, 2430-2440.
-
(1998)
Biochemistry
, vol.37
, pp. 2430-2440
-
-
Rowe, E.S.1
Zhang, F.2
Leung, T.W.3
Parr, J.S.4
Guy, P.T.5
-
72
-
-
77949399840
-
Mechanism and kinetics of peptide partitioning into membranes from all-atom simulations of thermostable peptides
-
Ulmschneider, M.B.; Doux, J.P.F.; Killian, J.A.; Smith, J.C.; Ulmschneider, J.P. Mechanism and kinetics of peptide partitioning into membranes from all-atom simulations of thermostable peptides. J. Am. Chem. Soc. 2010, 132, 3452-3460.
-
(2010)
J. Am. Chem. Soc.
, vol.132
, pp. 3452-3460
-
-
Ulmschneider, M.B.1
Doux, J.P.F.2
Killian, J.A.3
Smith, J.C.4
Ulmschneider, J.P.5
-
73
-
-
0003505419
-
-
IUPAC. Blackwell Scientific Publications: Oxford, UK
-
IUPAC. Compendium of Chemical Terminology, 2nd ed.; Blackwell Scientific Publications: Oxford, UK, 1997.
-
(1997)
Compendium of Chemical Terminology, 2nd ed
-
-
-
74
-
-
77955503561
-
Polarizable water model for the coarse-grained MARTINI force field
-
e1000810
-
Yesylevskyy, S.; Schäfer, L.; Sengupta, D.; Marrink, S. Polarizable water model for the coarse-grained MARTINI force field. PLoS Comput. Biol. 2010, 6, e1000810.
-
(2010)
PLoS Comput. Biol.
, vol.6
-
-
Yesylevskyy, S.1
Schäfer, L.2
Sengupta, D.3
Marrink, S.4
-
75
-
-
28544446125
-
Neutron and X-ray diffraction studies of liquids and glasses
-
doi:101088/0034-4885/69/1/r05
-
Fischer, H.E.; Barnes, A.C.; Salmon, P.S. Neutron and X-ray diffraction studies of liquids and glasses. Rep. Prog. Phys. 2006, 69, 233, doi:10.1088/0034-4885/69/1/r05.
-
(2006)
Rep. Prog. Phys.
, vol.69
, pp. 233
-
-
Fischer, H.E.1
Barnes, A.C.2
Salmon, P.S.3
-
76
-
-
51649129838
-
Lipid bilayer structure determined by the simultaneous analysis of neutron and X-ray scattering data
-
Kučerka, N.; Nagle, J.F.; Sachs, J.N.; Feller, S.E.; Pencer, J.; Jackson, A.; Katsaras, J. Lipid bilayer structure determined by the simultaneous analysis of neutron and X-ray scattering data. Biophys. J. 2008, 95, 2356-2367.
-
(2008)
Biophys. J.
, vol.95
, pp. 2356-2367
-
-
Kučerka, N.1
Nagle, J.F.2
Sachs, J.N.3
Feller, S.E.4
Pencer, J.5
Jackson, A.6
Katsaras, J.7
-
77
-
-
47749126522
-
Liquid-liquid domains in bilayers detected by wide angle X-ray scattering
-
Mills, T.T.; Tristram-Nagle, S.; Heberle, F.A.; Morales, N.F.; Zhao, J.; Wu, J.; Toombes, G.E.; Nagle, J.F.; Feigenson, G.W. Liquid-liquid domains in bilayers detected by wide angle X-ray scattering. Biophys. J. 2008, 95, 682-690.
-
(2008)
Biophys. J.
, vol.95
, pp. 682-690
-
-
Mills, T.T.1
Tristram-Nagle, S.2
Heberle, F.A.3
Morales, N.F.4
Zhao, J.5
Wu, J.6
Toombes, G.E.7
Nagle, J.F.8
Feigenson, G.W.9
-
78
-
-
70349487385
-
Experimental verification of lipid bilayer structure through multi-scale modeling
-
Perlmutter, J.D.; Sachs, J.N. Experimental verification of lipid bilayer structure through multi-scale modeling. Biochim. Biophys. Acta, Biomembr. 2009, 1788, 2284-2290.
-
(2009)
Biochim. Biophys. Acta, Biomembr.
, vol.1788
, pp. 2284-2290
-
-
Perlmutter, J.D.1
Sachs, J.N.2
-
79
-
-
84869067020
-
Molecular dynamics simulations of phosphatidylcholine membranes: A comparative force field study
-
Piggot, T.J.; Piñeiro, Á .; Khalid, S. Molecular dynamics simulations of phosphatidylcholine membranes: A comparative force field study. J. Chem. Theory Comput. 2012, 8, 4593-4609.
-
(2012)
J. Chem. Theory Comput.
, vol.8
, pp. 4593-4609
-
-
Piggot, T.J.1
Piñeiro, Á.2
Khalid, S.3
-
80
-
-
0016283654
-
Dynamic structure of fatty acyl chains in a phospholipid bilayer measured by deuterium magnetic resonance
-
Seelig, A.; Seelig, J. Dynamic structure of fatty acyl chains in a phospholipid bilayer measured by deuterium magnetic resonance. Biochemistry 1974, 13, 4839-4845.
-
(1974)
Biochemistry
, vol.13
, pp. 4839-4845
-
-
Seelig, A.1
Seelig, J.2
-
81
-
-
0344955341
-
Structures and transitions in lipid monolayers at the air-water interface
-
McConnell, H.M. Structures and transitions in lipid monolayers at the air-water interface. Annu. Rev. Phys. Chem. 1991, 42, 171-195.
-
(1991)
Annu. Rev. Phys. Chem.
, vol.42
, pp. 171-195
-
-
Mcconnell, H.M.1
-
82
-
-
0030783371
-
The mechanism of lamellar-to-inverted hexagonal phase transitions in phosphatidylethanolamine: Implications for membrane fusion mechanisms
-
Siegel, D.; Epand, R. The mechanism of lamellar-to-inverted hexagonal phase transitions in phosphatidylethanolamine: Implications for membrane fusion mechanisms. Biophys. J. 1997, 73, 3089-3111.
-
(1997)
Biophys. J.
, vol.73
, pp. 3089-3111
-
-
Siegel, D.1
Epand, R.2
-
83
-
-
0034321726
-
Thermodynamics and kinetics of the early steps of solid-state nucleation in the fluid lipid bilayer
-
Kharakoz, D.P.; Shlyapnikova, E.A. Thermodynamics and kinetics of the early steps of solid-state nucleation in the fluid lipid bilayer. J. Phys. Chem. B 2000, 104, 10368-10378.
-
(2000)
J. Phys. Chem. B
, vol.104
, pp. 10368-10378
-
-
Kharakoz, D.P.1
Shlyapnikova, E.A.2
-
84
-
-
37249073561
-
Pressure-area isotherm of a lipid monolayer from molecular dynamics simulations
-
Baoukina, S.; Monticelli, L.; Marrink, S.J.; Tieleman, D.P. Pressure-area isotherm of a lipid monolayer from molecular dynamics simulations. Langmuir 2007, 23, 12617-12623.
-
(2007)
Langmuir
, vol.23
, pp. 12617-12623
-
-
Baoukina, S.1
Monticelli, L.2
Marrink, S.J.3
Tieleman, D.P.4
-
85
-
-
49449107938
-
The molecular mechanism of lipid monolayer collapse
-
Baoukina, S.; Monticelli, L.; Risselada, H.J.; Marrink, S.J.; Tieleman, D.P. The molecular mechanism of lipid monolayer collapse. Proc. Natl. Acad. Sci. USA 2008, 105, 10803-10808.
-
(2008)
Proc. Natl. Acad. Sci. USA
, vol.105
, pp. 10803-10808
-
-
Baoukina, S.1
Monticelli, L.2
Risselada, H.J.3
Marrink, S.J.4
Tieleman, D.P.5
-
86
-
-
0242331729
-
Imaging coexisting fluid domains in biomembrane models coupling curvature and line tension
-
Baumgart, T.; Hess, S.T.;Webb,W.W. Imaging coexisting fluid domains in biomembrane models coupling curvature and line tension. Nature 2003, 425, 821-824.
-
(2003)
Nature
, vol.425
, pp. 821-824
-
-
Baumgart, T.1
Hess, S.T.2
Webb, W.W.3
-
87
-
-
34547260394
-
Line tension at fluid membrane domain boundaries measured by micropipette aspiration
-
208102:1-208102:4
-
Tian, A.; Johnson, C.; Wang, W.; Baumgart, T. Line tension at fluid membrane domain boundaries measured by micropipette aspiration. Phys. Rev. Lett. 2007, 98, 208102:1-208102:4.
-
(2007)
Phys. Rev. Lett.
, vol.98
-
-
Tian, A.1
Johnson, C.2
Wang, W.3
Baumgart, T.4
-
88
-
-
17544375815
-
Methodological problems in pressure profile calculations for lipid bilayers
-
124903:1-124903:9
-
Sonne, J.; Hansen, F.Y.; Peters, G.H. Methodological problems in pressure profile calculations for lipid bilayers. J. Chem. Phys. 2005, 122, 124903:1-124903:9.
-
(2005)
J. Chem. Phys.
, vol.122
-
-
Sonne, J.1
Hansen, F.Y.2
Peters, G.H.3
-
89
-
-
33645770992
-
Effect of average phospholipid curvature on supported bilayer formation on glass by vesicle fusion
-
Hamai, C.; Yang, T.; Kataoka, S.; Cremer, P.S.; Musser, S.M. Effect of average phospholipid curvature on supported bilayer formation on glass by vesicle fusion. Biophys. J. 2006, 90, 1241-1248.
-
(2006)
Biophys. J.
, vol.90
, pp. 1241-1248
-
-
Hamai, C.1
Yang, T.2
Kataoka, S.3
Cremer, P.S.4
Musser, S.M.5
-
90
-
-
61349109472
-
3D pressure field in lipid membranes and membrane-protein complexes
-
078101:1-078101:4
-
Ollila, O.H.S.; Risselada, H.J.; Louhivuori, M.; Lindahl, E.; Vattulainen, I.; Marrink, S.J. 3D pressure field in lipid membranes and membrane-protein complexes. Phys. Rev. Lett. 2009, 102, 078101:1-078101:4.
-
(2009)
Phys. Rev. Lett.
, vol.102
-
-
Ollila, O.H.S.1
Risselada, H.J.2
Louhivuori, M.3
Lindahl, E.4
Vattulainen, I.5
Marrink, S.J.6
-
91
-
-
0034271962
-
Spatial and energetic-entropic decomposition of surface tension in lipid bilayers from molecular dynamics simulations
-
Lindahl, E.; Edholm, O. Spatial and energetic-entropic decomposition of surface tension in lipid bilayers from molecular dynamics simulations. J. Chem. Phys. 2000, 113, 3882-3893.
-
(2000)
J. Chem. Phys.
, vol.113
, pp. 3882-3893
-
-
Lindahl, E.1
Edholm, O.2
-
92
-
-
0029737564
-
What is the surface tension of a lipid bilayer membrane?
-
Jähnig, F. What is the surface tension of a lipid bilayer membrane? Biophys. J. 1996, 71, 1348-1349.
-
(1996)
Biophys. J.
, vol.71
, pp. 1348-1349
-
-
Jähnig, F.1
-
93
-
-
0032614136
-
Constant surface tension simulations of lipid bilayers: The sensitivity of surface areas and compressibilities
-
Feller, S.E.; Pastor, R.W. Constant surface tension simulations of lipid bilayers: The sensitivity of surface areas and compressibilities. J. Chem. Phys. 1999, 111, 1281-1287.
-
(1999)
J. Chem. Phys.
, vol.111
, pp. 1281-1287
-
-
Feller, S.E.1
Pastor, R.W.2
-
94
-
-
0035812110
-
Effect of undulations on surface tension in simulated bilayers
-
Marrink, S.J.; Mark, A.E. Effect of undulations on surface tension in simulated bilayers. J. Phys. Chem. B 2001, 105, 6122-6127.
-
(2001)
J. Phys. Chem. B
, vol.105
, pp. 6122-6127
-
-
Marrink, S.J.1
Mark, A.E.2
-
95
-
-
34250372191
-
Reparameterization of all-atom dipalmitoylphosphatidylcholine lipid parameters enables simulation of fluid bilayers at zero tension
-
Sonne, J.; Jensen, M.Ø.; Hansen, F.Y.; Hemmingsen, L.; Peters, G.H. Reparameterization of all-atom dipalmitoylphosphatidylcholine lipid parameters enables simulation of fluid bilayers at zero tension. Biophys. J. 2007, 92, 4157-4167.
-
(2007)
Biophys. J.
, vol.92
, pp. 4157-4167
-
-
Sonne, J.1
Jensen, M.Ø.2
Hansen, F.Y.3
Hemmingsen, L.4
Peters, G.H.5
-
96
-
-
84943997802
-
Elastic properties of lipid bilayers: Theory and possible experiments
-
Helfrich, W. Elastic properties of lipid bilayers: Theory and possible experiments. Z. Naturforsch. C Biosci. 1973, 28, 693-703.
-
(1973)
Z. Naturforsch. C Biosci.
, vol.28
, pp. 693-703
-
-
Helfrich, W.1
-
97
-
-
0001153511
-
The bending rigidity of phosphatidylcholine bilayers: Dependences on experimental method, sample cell sealing and temperature
-
Niggemann, G.; Kummrow, M.; Helfrich, W. The bending rigidity of phosphatidylcholine bilayers: Dependences on experimental method, sample cell sealing and temperature. J. Phys. II Fr. 1995, 5, 413-425.
-
(1995)
J. Phys. II Fr.
, vol.5
, pp. 413-425
-
-
Niggemann, G.1
Kummrow, M.2
Helfrich, W.3
-
98
-
-
0000361471
-
Deformation of giant lipid bilayer vesicles in shear flow
-
De Haas, K.H.; Blom, C.; van den Ende, D.; Duits, M.H.G.; Mellema, J. Deformation of giant lipid bilayer vesicles in shear flow. Phys. Rev. E 1997, 56, 7132-7137.
-
(1997)
Phys. Rev. E
, vol.56
, pp. 7132-7137
-
-
De Haas, K.H.1
Blom, C.2
Van den Ende, D.3
Duits, M.H.G.4
Mellema, J.5
-
99
-
-
0033932837
-
Effect of chain length and unsaturation on elasticity of lipid bilayers
-
Rawicz, W.; Olbrich, K.; McIntosh, T.; Needham, D.; Evans, E. Effect of chain length and unsaturation on elasticity of lipid bilayers. Biophys. J. 2000, 79, 328-339.
-
(2000)
Biophys. J.
, vol.79
, pp. 328-339
-
-
Rawicz, W.1
Olbrich, K.2
Mcintosh, T.3
Needham, D.4
Evans, E.5
-
100
-
-
0033932839
-
Mesoscopic undulations and thickness fluctuations in lipid bilayers from molecular dynamics simulations
-
Lindahl, E.; Edholm, O. Mesoscopic undulations and thickness fluctuations in lipid bilayers from molecular dynamics simulations. Biophys. J. 2000, 79, 426-433.
-
(2000)
Biophys. J.
, vol.79
, pp. 426-433
-
-
Lindahl, E.1
Edholm, O.2
-
101
-
-
79959741351
-
Interpretation of fluctuation spectra in lipid bilayer simulations
-
Brandt, E.G.; Braun, A.R.; Sachs, J.N.; Nagle, J.F.; Edholm, O. Interpretation of fluctuation spectra in lipid bilayer simulations. Biophys. J. 2011, 100, 2104-2111.
-
(2011)
Biophys. J.
, vol.100
, pp. 2104-2111
-
-
Brandt, E.G.1
Braun, A.R.2
Sachs, J.N.3
Nagle, J.F.4
Edholm, O.5
-
102
-
-
33751577958
-
A novel method for measuring the bending rigidity of model lipid membranes by simulating tethers
-
204905:1-204905:6
-
Harmandaris, V.A.; Deserno, M. A novel method for measuring the bending rigidity of model lipid membranes by simulating tethers. J. Chem. Phys. 2006, 125, 204905:1-204905:6.
-
(2006)
J. Chem. Phys.
, vol.125
-
-
Harmandaris, V.A.1
Deserno, M.2
-
103
-
-
0141642121
-
Sphingomyelin/phosphatidylcholine/cholesterol phase diagram: Boundaries and composition of lipid rafts
-
De Almeida, R.F.; Fedorov, A.; Prieto, M. Sphingomyelin/phosphatidylcholine/cholesterol phase diagram: Boundaries and composition of lipid rafts. Biophys. J. 2003, 85, 2406-2416.
-
(2003)
Biophys. J.
, vol.85
, pp. 2406-2416
-
-
De Almeida, R.F.1
Fedorov, A.2
Prieto, M.3
-
104
-
-
2142643656
-
Cholesterol-phospholipid interactions, the liquid-ordered phase and lipid rafts in model and biological membranes
-
McMullen, T.P.; Lewis, R.N.; McElhaney, R.N. Cholesterol-phospholipid interactions, the liquid-ordered phase and lipid rafts in model and biological membranes. Curr. Opin. Colloid Interface Sci. 2004, 8, 459-468.
-
(2004)
Curr. Opin. Colloid Interface Sci.
, vol.8
, pp. 459-468
-
-
Mcmullen, T.P.1
Lewis, R.N.2
Mcelhaney, R.N.3
-
105
-
-
53249125167
-
Four-scale description of membrane sculpting by BAR domains
-
Arkhipov, A.; Yin, Y.; Schulten, K. Four-scale description of membrane sculpting by BAR domains. Biophys. J. 2008, 95, 2806-2821.
-
(2008)
Biophys. J.
, vol.95
, pp. 2806-2821
-
-
Arkhipov, A.1
Yin, Y.2
Schulten, K.3
-
106
-
-
66349103875
-
Simulations of membrane tubulation by lattices of amphiphysin N-BAR domains
-
Yin, Y.; Arkhipov, A.; Schulten, K. Simulations of membrane tubulation by lattices of amphiphysin N-BAR domains. Structure 2009, 17, 882-892.
-
(2009)
Structure
, vol.17
, pp. 882-892
-
-
Yin, Y.1
Arkhipov, A.2
Schulten, K.3
-
107
-
-
78650543009
-
Release of content through mechano-sensitive gates in pressurized liposomes
-
Louhivuori, M.; Risselada, H.J.; van der Giessen, E.; Marrink, S.J. Release of content through mechano-sensitive gates in pressurized liposomes. Proc. Natl. Acad. Sci. USA 2010, 107, 19856-19860.
-
(2010)
Proc. Natl. Acad. Sci. USA
, vol.107
, pp. 19856-19860
-
-
Louhivuori, M.1
Risselada, H.J.2
Van der Giessen, E.3
Marrink, S.J.4
-
108
-
-
18744371588
-
Molecular dynamics and protein function
-
Karplus, M.; Kuriyan, J. Molecular dynamics and protein function. Proc. Natl. Acad. Sci. USA 2005, 102, 6679-6685.
-
(2005)
Proc. Natl. Acad. Sci. USA
, vol.102
, pp. 6679-6685
-
-
Karplus, M.1
Kuriyan, J.2
-
109
-
-
0036725277
-
Molecular dynamics simulations of biomolecules
-
Karplus, M.; McCammon, J.A. Molecular dynamics simulations of biomolecules. Nat. Struct. Mol. Biol. 2002, 9, 646-652.
-
(2002)
Nat. Struct. Mol. Biol.
, vol.9
, pp. 646-652
-
-
Karplus, M.1
Mccammon, J.A.2
-
110
-
-
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
-
111
-
-
84863307801
-
Computational models of protein kinematics and dynamics: Beyond simulation
-
Gipson, B.; Hsu, D.; Kavraki, L.E.; Latombe, J.C. Computational models of protein kinematics and dynamics: Beyond simulation. Annu. Rev. Anal. Chem. 2012, 5, 273-291.
-
(2012)
Annu. Rev. Anal. Chem.
, vol.5
, pp. 273-291
-
-
Gipson, B.1
Hsu, D.2
Kavraki, L.E.3
Latombe, J.C.4
-
112
-
-
80054950510
-
Molecular dynamics simulations and drug discovery
-
doi:10.1186/1741-7007-9-71
-
Durrant, J.; McCammon, J.A. Molecular dynamics simulations and drug discovery. BMC Biol. 2011, 9, 71. doi:10.1186/1741-7007-9-71.
-
(2011)
BMC Biol.
, vol.9
, pp. 71
-
-
Durrant, J.1
Mccammon, J.A.2
-
113
-
-
77952938726
-
Global dynamics of proteins: Bridging between structure and function
-
Bahar, I.; Lezon, T.R.; Yang, L.W.; Eyal, E. Global dynamics of proteins: Bridging between structure and function. Annu. Rev. Biophys. 2010, 39, 23-42.
-
(2010)
Annu. Rev. Biophys.
, vol.39
, pp. 23-42
-
-
Bahar, I.1
Lezon, T.R.2
Yang, L.W.3
Eyal, E.4
-
114
-
-
33646943202
-
Molecular dynamics: Survey of methods for simulating the activity of proteins
-
Adcock, S.; McCammon, J. 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.1
Mccammon, J.2
-
115
-
-
84861367246
-
Biomolecular simulation: A computational microscope for molecular biology
-
Dror, R.O.; Dirks, R.M.; Grossman, J.P.; Xu, H.; Shaw, D.E. Biomolecular simulation: A computational microscope for molecular biology. Annu. Rev. Biophys. 2012, 41, 429-452.
-
(2012)
Annu. Rev. Biophys.
, vol.41
, pp. 429-452
-
-
Dror, R.O.1
Dirks, R.M.2
Grossman, J.P.3
Xu, H.4
Shaw, D.E.5
-
116
-
-
84934440741
-
Comparison of Protein Force Fields for Molecular Dynamics Simulations
-
Humana Press: New York, NY, USA
-
Guvench, O.; MacKerell, Alexander D., J. Comparison of Protein Force Fields for Molecular Dynamics Simulations. In Methods Molecular Biology; Kukol, A., Ed.; Humana Press: New York, NY, USA, 2008; Volume 443, pp. 63-88.
-
(2008)
In Methods Molecular Biology; Kukol, A., Ed.
, vol.443
, pp. 63-88
-
-
Guvench, O.1
MacKerell, A.D.J.2
-
117
-
-
79959720287
-
How robust are protein folding simulations with respect to force field parameterization?
-
Piana, S.; Lindorff-Larsen, K.; Shaw, D. How robust are protein folding simulations with respect to force field parameterization? Biophys. J. 2011, 100, L47-L49.
-
(2011)
Biophys. J.
, vol.100
-
-
Piana, S.1
Lindorff-Larsen, K.2
Shaw, D.3
-
118
-
-
84857463877
-
Systematic validation of protein force fields against experimental data
-
Lindorff-Larsen, K.; Maragakis, P.; Piana, S.; Eastwood, M.P.; Dror, R.O.; Shaw, D.E. Systematic validation of protein force fields against experimental data. PLoS One 2012, 7, e32131.
-
(2012)
PLoS One
, vol.7
-
-
Lindorff-Larsen, K.1
Maragakis, P.2
Piana, S.3
Eastwood, M.P.4
Dror, R.O.5
Shaw, D.E.6
-
119
-
-
84859611714
-
Are protein force fields getting better? A systematic benchmark on 524 diverse NMR measurements
-
Beauchamp, K.A.; Lin, Y.S.; Das, R.; Pande, V.S. Are protein force fields getting better? A systematic benchmark on 524 diverse NMR measurements. J. Chem. Theory Comput. 2012, 8, 1409-1414.
-
(2012)
J. Chem. Theory Comput.
, vol.8
, pp. 1409-1414
-
-
Beauchamp, K.A.1
Lin, Y.S.2
Das, R.3
Pande, V.S.4
-
120
-
-
0037038372
-
Absolute comparison of simulated and experimental protein-folding dynamics
-
Snow, C.D.; Nguyen, H.; Pande, V.S.; Gruebele, M. Absolute comparison of simulated and experimental protein-folding dynamics. Nature 2002, 420, 102-106.
-
(2002)
Nature
, vol.420
, pp. 102-106
-
-
Snow, C.D.1
Nguyen, H.2
Pande, V.S.3
Gruebele, M.4
-
121
-
-
84869761071
-
The protein-folding problem, 50 years on
-
Dill, K.A.; MacCallum, J.L. The protein-folding problem, 50 years on. Science 2012, 338, 1042-1046.
-
(2012)
Science
, vol.338
, pp. 1042-1046
-
-
Dill, K.A.1
Maccallum, J.L.2
-
122
-
-
79955013716
-
Making connections between ultrafast protein folding kinetics and molecular dynamics simulations
-
Cellmer, T.; Buscaglia, M.; Henry, E.R.; Hofrichter, J.; Eaton,W.A. Making connections between ultrafast protein folding kinetics and molecular dynamics simulations. Proc. Natl. Acad. Sci. USA 2011, 108, 6103-6108.
-
(2011)
Proc. Natl. Acad. Sci. USA
, vol.108
, pp. 6103-6108
-
-
Cellmer, T.1
Buscaglia, M.2
Henry, E.R.3
Hofrichter, J.4
Eaton, W.A.5
-
123
-
-
77951270272
-
Large conformational changes in proteins: Signaling and other functions
-
Grant, B.J.; Gorfe, A.A.; McCammon, J.A. Large conformational changes in proteins: Signaling and other functions. Curr. Opin. Struct. Biol. 2010, 20, 142-147.
-
(2010)
Curr. Opin. Struct. Biol.
, vol.20
, pp. 142-147
-
-
Grant, B.J.1
Gorfe, A.A.2
Mccammon, J.A.3
-
124
-
-
34249930405
-
Protein-folding dynamics: Overview of molecular simulation techniques
-
Scheraga, H.A.; Khalili, M.; Liwo, A. Protein-folding dynamics: Overview of molecular simulation techniques. Annu. Rev. Phys. Chem. 2007, 58, 57-83.
-
(2007)
Annu. Rev. Phys. Chem.
, vol.58
, pp. 57-83
-
-
Scheraga, H.A.1
Khalili, M.2
Liwo, A.3
-
125
-
-
84858621382
-
Structural modelling and dynamics of proteins for insights into drug interactions
-
Werner, T.; Morris, M.B.; Dastmalchi, S.; Church, W.B. Structural modelling and dynamics of proteins for insights into drug interactions. Adv. Drug Deliv. Rev. 2012, 64, 323-343.
-
(2012)
Adv. Drug Deliv. Rev.
, vol.64
, pp. 323-343
-
-
Werner, T.1
Morris, M.B.2
Dastmalchi, S.3
Church, W.B.4
-
126
-
-
33748276474
-
Protein-ligand docking: Current status and future challenges
-
Sousa, S.F.; Fernandes, P.A.; Ramos, M.J. Protein-ligand docking: Current status and future challenges. Proteins 2006, 65, 15-26.
-
(2006)
Proteins
, vol.65
, pp. 15-26
-
-
Sousa, S.F.1
Fernandes, P.A.2
Ramos, M.J.3
-
127
-
-
79960218748
-
Efficient incorporation of protein flexibility and dynamics into molecular docking simulations
-
Lill, M.A. Efficient incorporation of protein flexibility and dynamics into molecular docking simulations. Biochemistry 2011, 50, 6157-6169.
-
(2011)
Biochemistry
, vol.50
, pp. 6157-6169
-
-
Lill, M.A.1
-
128
-
-
78149495374
-
Molecular dynamics simulations of protein dynamics and their relevance to drug discovery
-
Salsbury, F.R., Jr. Molecular dynamics simulations of protein dynamics and their relevance to drug discovery. Curr. Opin. Pharmacol. 2010, 10, 738-744.
-
(2010)
Curr. Opin. Pharmacol.
, vol.10
, pp. 738-744
-
-
Salsbury Jr., F.R.1
-
129
-
-
78149500703
-
Protein dynamics: Dancing on an ever-changing free energy stage
-
Livesay, D.R. Protein dynamics: Dancing on an ever-changing free energy stage. Curr. Opin. Pharmacol. 2010, 10, 706-708.
-
(2010)
Curr. Opin. Pharmacol.
, vol.10
, pp. 706-708
-
-
Livesay, D.R.1
-
130
-
-
84857131975
-
Disordered proteins and network disorder in network descriptions of protein structure, dynamics and function: Hypotheses and a comprehensive review
-
Csermely, P.; Singh Sandhu, K.; Hazai, E.; Hoksza, Z.; Kiss, H.J.M.; Miozzo, F.; Veres, D.V.; Piazza, F.; Nussinov, R. Disordered proteins and network disorder in network descriptions of protein structure, dynamics and function: Hypotheses and a comprehensive review. Curr. Protein Pept. Sci. 2011, 13, 19-33.
-
(2011)
Curr. Protein Pept. Sci.
, vol.13
, pp. 19-33
-
-
Csermely, P.1
Singh Sandhu, K.2
Hazai, E.3
Hoksza, Z.4
Kiss, H.J.M.5
Miozzo, F.6
Veres, D.V.7
Piazza, F.8
Nussinov, R.9
-
131
-
-
79953075221
-
Alchemical free energy methods for drug discovery: Progress and challenges
-
Chodera, J.D.; Mobley, D.L.; Shirts, M.R.; Dixon, R.W.; Branson, K.; Pande, V.S. Alchemical free energy methods for drug discovery: Progress and challenges. Curr. Opin. Struct. Biol. 2011, 21, 150-160.
-
(2011)
Curr. Opin. Struct. Biol.
, vol.21
, pp. 150-160
-
-
Chodera, J.D.1
Mobley, D.L.2
Shirts, M.R.3
Dixon, R.W.4
Branson, K.5
Pande, V.S.6
-
132
-
-
77958083861
-
Protein mechanics: From single molecules to functional biomaterials
-
Li, H.; Cao, Y. Protein mechanics: From single molecules to functional biomaterials. Acc. Chem. Res. 2010, 43, 1331-1341.
-
(2010)
Acc. Chem. Res.
, vol.43
, pp. 1331-1341
-
-
Li, H.1
Cao, Y.2
-
133
-
-
70349779536
-
Discovery through the computational microscope
-
Lee, E.; Hsin, J.; Sotomayor, M.; Comellas, G.; Schulten, K. Discovery through the computational microscope. Structure 2009, 17, 1295-1306.
-
(2009)
Structure
, vol.17
, pp. 1295-1306
-
-
Lee, E.1
Hsin, J.2
Sotomayor, M.3
Comellas, G.4
Schulten, K.5
-
134
-
-
79960007037
-
Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations
-
Buch, I.; Giorgino, T.; de Fabritiis, G. Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations. Proc. Natl. Acad. Sci. USA 2011, 108, 10184-10189.
-
(2011)
Proc. Natl. Acad. Sci. USA
, vol.108
, pp. 10184-10189
-
-
Buch, I.1
Giorgino, T.2
De Fabritiis, G.3
-
135
-
-
84863533518
-
Multiple molecule effects on the cooperativity of protein folding transitions in simulations
-
245101:1-245101:10
-
Lewis, J.I.; Moss, D.J.; Knotts, T.A. Multiple molecule effects on the cooperativity of protein folding transitions in simulations. J. Chem. Phys. 2012, 136, 245101:1-245101:10.
-
(2012)
J. Chem. Phys.
, vol.136
-
-
Lewis, J.I.1
Moss, D.J.2
Knotts, T.A.3
-
136
-
-
78149423038
-
Formation of salt bridges mediates internal dimerization of myosin VI medial tail domain
-
Kim, H.; Hsin, J.; Liu, Y.; Selvin, P.R.; Schulten, K. Formation of salt bridges mediates internal dimerization of myosin VI medial tail domain. Structure 2010, 18, 1443-1449.
-
(2010)
Structure
, vol.18
, pp. 1443-1449
-
-
Kim, H.1
Hsin, J.2
Liu, Y.3
Selvin, P.R.4
Schulten, K.5
-
137
-
-
78349275327
-
Non-bulk-like solvent behavior in the ribosome exit tunnel
-
e1000963
-
Lucent, D.; Snow, C.D.; Aitken, C.E.; Pande, V.S. Non-bulk-like solvent behavior in the ribosome exit tunnel. PLoS Comput. Biol. 2010, 6, e1000963.
-
(2010)
PLoS Comput. Biol.
, vol.6
-
-
Lucent, D.1
Snow, C.D.2
Aitken, C.E.3
Pande, V.S.4
-
138
-
-
84865283412
-
Atomistic modeling of protein-DNA interaction specificity: Progress and applications
-
Liu, L.A.; Bradley, P. Atomistic modeling of protein-DNA interaction specificity: Progress and applications. Curr. Opin. Struct. Biol. 2012, 22, 397-405.
-
(2012)
Curr. Opin. Struct. Biol.
, vol.22
, pp. 397-405
-
-
Liu, L.A.1
Bradley, P.2
-
140
-
-
73349084983
-
Combining an elastic network with a coarse-grained molecular force field: Structure, dynamics, and intermolecular recognition
-
Periole, X.; Cavalli, M.; Marrink, S.J.; Ceruso, M.A. Combining an elastic network with a coarse-grained molecular force field: Structure, dynamics, and intermolecular recognition. J. Chem. Theory Comput. 2009, 5, 2531-2543.
-
(2009)
J. Chem. Theory Comput.
, vol.5
, pp. 2531-2543
-
-
Periole, X.1
Cavalli, M.2
Marrink, S.J.3
Ceruso, M.A.4
-
141
-
-
70449111604
-
Defining coarse-grained representations of large biomolecules and biomolecular complexes from elastic network models
-
Zhang, Z.; Pfaendtner, J.; Grafmüller, A.; Voth, G.A. Defining coarse-grained representations of large biomolecules and biomolecular complexes from elastic network models. Biophys. J. 2009, 97, 2327-2337.
-
(2009)
Biophys. J.
, vol.97
, pp. 2327-2337
-
-
Zhang, Z.1
Pfaendtner, J.2
Grafmüller, A.3
Voth, G.A.4
-
142
-
-
58149161251
-
Systematic multiscale parameterization of heterogeneous elastic network models of proteins
-
Lyman, E.; Pfaendtner, J.; Voth, G. Systematic multiscale parameterization of heterogeneous elastic network models of proteins. Biophys. J. 2008, 95, 4183-4192.
-
(2008)
Biophys. J.
, vol.95
, pp. 4183-4192
-
-
Lyman, E.1
Pfaendtner, J.2
Voth, G.3
-
143
-
-
78149495449
-
Reaching biological timescales with all-atom molecular dynamics simulations
-
Zwier, M.C.; Chong, L.T. Reaching biological timescales with all-atom molecular dynamics simulations. Curr. Opin. Pharmacol. 2010, 10, 745-752.
-
(2010)
Curr. Opin. Pharmacol.
, vol.10
, pp. 745-752
-
-
Zwier, M.C.1
Chong, L.T.2
-
144
-
-
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
-
145
-
-
73349117815
-
Mechanical signaling on the single protein level studied using steered molecular dynamics
-
Genchev, G.Z.; Källberg, M.; Gürsoy, G.; Mittal, A.; Dubey, L.; Perisic, O.; Feng, G.; Langlois, R.; Lu, H. Mechanical signaling on the single protein level studied using steered molecular dynamics. Cell Biochem. Biophys. 2009, 55, 141-152.
-
(2009)
Cell Biochem. Biophys.
, vol.55
, pp. 141-152
-
-
Genchev, G.Z.1
Källberg, M.2
Gürsoy, G.3
Mittal, A.4
Dubey, L.5
Perisic, O.6
Feng, G.7
Langlois, R.8
Lu, H.9
-
146
-
-
58149299971
-
Metadynamics: A method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science
-
doi:101088/0034-4885/71/12/126601
-
Laio, A.; Gervasio, F.L. Metadynamics: A method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science. Rep. Prog. Phys. 2008, 71, doi:10.1088/0034-4885/71/12/126601.
-
(2008)
Rep. Prog. Phys.
, vol.71
-
-
Laio, A.1
Gervasio, F.L.2
-
147
-
-
33745762636
-
A temperature accelerated method for sampling free energy and determining reaction pathways in rare events simulations
-
Maragliano, L.; Vanden-Eijnden, E. A temperature accelerated method for sampling free energy and determining reaction pathways in rare events simulations. Chem. Phys. Lett. 2006, 426, 168-175.
-
(2006)
Chem. Phys. Lett.
, vol.426
, pp. 168-175
-
-
Maragliano, L.1
Vanden-Eijnden, E.2
-
148
-
-
79960998152
-
Free energy calculations of protein-ligand interactions
-
De Ruiter, A.; Oostenbrink, C. Free energy calculations of protein-ligand interactions. Curr. Opin. Chem. Biol. 2011, 15, 547-552.
-
(2011)
Curr. Opin. Chem. Biol.
, vol.15
, pp. 547-552
-
-
De Ruiter, A.1
Oostenbrink, C.2
-
149
-
-
85013130546
-
Monte carlo studies of protein aggregation
-
Jónsson, S.; Staneva, I.; Mohanty, S.; Irbäck, A. Monte carlo studies of protein aggregation. Phys. Procedia 2012, 34, 49-54.
-
(2012)
Phys. Procedia
, vol.34
, pp. 49-54
-
-
Jónsson, S.1
Staneva, I.2
Mohanty, S.3
Irbäck, A.4
-
150
-
-
84874942220
-
Mixed monte carlo-molecular dynamics simulations of the prion protein
-
Ribeiro, A.A.; de Alencastro, R.B. Mixed monte carlo-molecular dynamics simulations of the prion protein. J. Mol. Graphics Modell. 2013, 42, 1-6.
-
(2013)
J. Mol. Graphics Modell.
, vol.42
, pp. 1-6
-
-
Ribeiro, A.A.1
De Alencastro, R.B.2
-
151
-
-
75349094390
-
Molecular simulation of adsorption and its implications to protein chromatography: A review
-
Zhang, L.; Sun, Y. Molecular simulation of adsorption and its implications to protein chromatography: A review. Biochem. Eng. J. 2010, 48, 408-415.
-
(2010)
Biochem. Eng. J.
, vol.48
, pp. 408-415
-
-
Zhang, L.1
Sun, Y.2
-
152
-
-
78149500243
-
Using NMR to study fast dynamics in proteins: Methods and applications
-
Sapienza, P.J.; Lee, A.L. Using NMR to study fast dynamics in proteins: Methods and applications. Curr. Opin. Pharmacol. 2010, 10, 723-730.
-
(2010)
Curr. Opin. Pharmacol.
, vol.10
, pp. 723-730
-
-
Sapienza, P.J.1
Lee, A.L.2
-
153
-
-
82455216908
-
Combining NMR and Molecular Dynamics Studies for Insights into the Allostery of Small GTPase-Protein Interactions
-
Springer: New York, NY, USA
-
Zhang, L.; Bouguet-Bonnet, S.; Buck, M. Combining NMR and Molecular Dynamics Studies for Insights into the Allostery of Small GTPase-Protein Interactions. In Methods in Molecular Biology; Fenton, A.W., Ed.; Springer: New York, NY, USA, 2012; Volume 796, pp. 235-259.
-
(2012)
In Methods in Molecular Biology; Fenton, A.W., Ed.
, vol.796
, pp. 235-259
-
-
Zhang, L.1
Bouguet-Bonnet, S.2
Buck, M.3
-
154
-
-
54949109484
-
The relative entropy is fundamental to multiscale and inverse thermodynamic problems
-
144108:1-144108:7
-
Shell, M.S. The relative entropy is fundamental to multiscale and inverse thermodynamic problems. J. Chem. Phys. 2008, 129, 144108:1-144108:7.
-
(2008)
J. Chem. Phys.
, vol.129
-
-
Shell, M.S.1
-
155
-
-
7044224837
-
Computer simulations of membrane proteins
-
Ash, W.L.; Zlomislic, M.R.; Oloo, E.O.; Tieleman, D.P. Computer simulations of membrane proteins. Biochim. Biophys. Acta Biomembr. 2004, 1666, 158-189.
-
(2004)
Biochim. Biophys. Acta Biomembr.
, vol.1666
, pp. 158-189
-
-
Ash, W.L.1
Zlomislic, M.R.2
Oloo, E.O.3
Tieleman, D.P.4
-
156
-
-
49549083949
-
Membrane proteins: Molecular dynamics simulations
-
Lindahl, E.; Sansom, M.S. Membrane proteins: Molecular dynamics simulations. Curr. Opin. Struct. Biol. 2008, 18, 425-431.
-
(2008)
Curr. Opin. Struct. Biol.
, vol.18
, pp. 425-431
-
-
Lindahl, E.1
Sansom, M.S.2
-
157
-
-
84872926726
-
Molecular modeling and simulation of membrane lipid-mediated effects on GPCRs
-
Sadiq, S.; Guixa-Gonzalez, R.; Dainese, E.; Pastor, M.; de Fabritiis, G.; Selent, J. Molecular modeling and simulation of membrane lipid-mediated effects on GPCRs. Curr. Med. Chem. 2013, 20, 22-38.
-
(2013)
Curr. Med. Chem.
, vol.20
, pp. 22-38
-
-
Sadiq, S.1
Guixa-Gonzalez, R.2
Dainese, E.3
Pastor, M.4
De Fabritiis, G.5
Selent, J.6
-
158
-
-
77953739333
-
Atomistic simulation of hydrophobic matching effects on lipid composition near a helical peptide embedded in mixed-lipid bilayers
-
Yin, F.; Kindt, J.T. Atomistic simulation of hydrophobic matching effects on lipid composition near a helical peptide embedded in mixed-lipid bilayers. J. Phys. Chem. B 2010, 114, 8076-8080.
-
(2010)
J. Phys. Chem. B
, vol.114
, pp. 8076-8080
-
-
Yin, F.1
Kindt, J.T.2
-
159
-
-
80052233358
-
All-atom and coarse-grained molecular dynamics simulations of a membrane protein stabilizing polymer
-
Perlmutter, J.D.; Drasler, W.J.; Xie, W.; Gao, J.; Popot, J.L.; Sachs, J.N. All-atom and coarse-grained molecular dynamics simulations of a membrane protein stabilizing polymer. Langmuir 2011, 27, 10523-10537.
-
(2011)
Langmuir
, vol.27
, pp. 10523-10537
-
-
Perlmutter, J.D.1
Drasler, W.J.2
Xie, W.3
Gao, J.4
Popot, J.L.5
Sachs, J.N.6
-
160
-
-
50349095199
-
The interaction of phospholipase A2 with a phospholipid bilayer: Coarse-grained molecular dynamics simulations
-
Wee, C.L.; Balali-Mood, K.; Gavaghan, D.; Sansom, M.S. The interaction of phospholipase A2 with a phospholipid bilayer: Coarse-grained molecular dynamics simulations. Biophys. J. 2008, 95, 1649-1657.
-
(2008)
Biophys. J.
, vol.95
, pp. 1649-1657
-
-
Wee, C.L.1
Balali-Mood, K.2
Gavaghan, D.3
Sansom, M.S.4
-
161
-
-
58149164577
-
Peptide aggregation and pore formation in a lipid bilayer: A combined coarse-grained and all atom molecular dynamics study
-
Thøgersen, L.; Schiøtt, B.; Vosegaard, T.; Nielsen, N.C.; Tajkhorshid, E. Peptide aggregation and pore formation in a lipid bilayer: A combined coarse-grained and all atom molecular dynamics study. Biophys. J. 2008, 95, 4337-4347.
-
(2008)
Biophys. J.
, vol.95
, pp. 4337-4347
-
-
Thøgersen, L.1
Schiøtt, B.2
Vosegaard, T.3
Nielsen, N.C.4
Tajkhorshid, E.5
-
162
-
-
62349089500
-
Self-assembling dipeptides: Conformational sampling in solvent-free coarse-grained simulation
-
Villa, A.; Peter, C.; van der Vegt, N.F.A. Self-assembling dipeptides: Conformational sampling in solvent-free coarse-grained simulation. Phys. Chem. Chem. Phys. 2009, 11, 2077-2086.
-
(2009)
Phys. Chem. Chem. Phys.
, vol.11
, pp. 2077-2086
-
-
Villa, A.1
Peter, C.2
Van der Vegt, N.F.A.3
-
163
-
-
77950584902
-
Reconstruction of atomistic details from coarse-grained structures
-
Rzepiela, A.J.; Schafer, L.V.; Goga, N.; Risselada, H.J.; de Vries, A.H.; Marrink, S.J. Reconstruction of atomistic details from coarse-grained structures. J. Comput. Chem. 2010, 31, 1333-1343.
-
(2010)
J. Comput. Chem.
, vol.31
, pp. 1333-1343
-
-
Rzepiela, A.J.1
Schafer, L.V.2
Goga, N.3
Risselada, H.J.4
De Vries, A.H.5
Marrink, S.J.6
-
164
-
-
84857447250
-
Multiscale simulation of small peptides: Consistent conformational sampling in atomistic and coarse-grained models
-
Bezkorovaynaya, O.; Lukyanov, A.; Kremer, K.; Peter, C. Multiscale simulation of small peptides: Consistent conformational sampling in atomistic and coarse-grained models. J. Comput. Chem. 2012, 33, 937-949.
-
(2012)
J. Comput. Chem.
, vol.33
, pp. 937-949
-
-
Bezkorovaynaya, O.1
Lukyanov, A.2
Kremer, K.3
Peter, C.4
-
165
-
-
0345743709
-
Protein topology determines binding mechanism
-
Levy, Y.; Wolynes, P.G.; Onuchic, J.N. Protein topology determines binding mechanism. Proc. Natl. Acad. Sci. USA 2004, 101, 511-516.
-
(2004)
Proc. Natl. Acad. Sci. USA
, vol.101
, pp. 511-516
-
-
Levy, Y.1
Wolynes, P.G.2
Onuchic, J.N.3
-
166
-
-
9244260521
-
Molecular dynamics simulations of spontaneous fibril formation by random-coil peptides
-
Nguyen, H.D.; Hall, C.K. Molecular dynamics simulations of spontaneous fibril formation by random-coil peptides. Proc. Natl. Acad. Sci. USA 2004, 101, 16180-16185.
-
(2004)
Proc. Natl. Acad. Sci. USA
, vol.101
, pp. 16180-16185
-
-
Nguyen, H.D.1
Hall, C.K.2
-
167
-
-
51649113464
-
Exploring the suitability of coarse-grained techniques for the representation of protein dynamics
-
Emperador, A.; Carrillo, O.; Rueda, M.; Orozco, M. Exploring the suitability of coarse-grained techniques for the representation of protein dynamics. Biophys. J. 2008, 95, 2127-2138.
-
(2008)
Biophys. J.
, vol.95
, pp. 2127-2138
-
-
Emperador, A.1
Carrillo, O.2
Rueda, M.3
Orozco, M.4
-
168
-
-
0037418340
-
Atomic-level observation of macromolecular crowding effects: Escape of a protein from the GroEL cage
-
Elcock, A.H. Atomic-level observation of macromolecular crowding effects: Escape of a protein from the GroEL cage. Proc. Natl. Acad. Sci. USA 2003, 100, 2340-2344.
-
(2003)
Proc. Natl. Acad. Sci. USA
, vol.100
, pp. 2340-2344
-
-
Elcock, A.H.1
-
169
-
-
25844431698
-
Coarse-grained normal mode analysis in structural biology
-
Bahar, I.; Rader, A. Coarse-grained normal mode analysis in structural biology. Curr. Opin. Struct. Biol. 2005, 15, 586-592.
-
(2005)
Curr. Opin. Struct. Biol.
, vol.15
, pp. 586-592
-
-
Bahar, I.1
Rader, A.2
-
170
-
-
0037398844
-
Minimalist models for protein folding and design
-
Head-Gordon, T.; Brown, S. Minimalist models for protein folding and design. Curr. Opin. Struct. Biol. 2003, 13, 160-167.
-
(2003)
Curr. Opin. Struct. Biol.
, vol.13
, pp. 160-167
-
-
Head-Gordon, T.1
Brown, S.2
-
171
-
-
79959807226
-
A coarse-grained approach to protein design: Learning from design to understand folding
-
e20853
-
Coluzza, I. A coarse-grained approach to protein design: Learning from design to understand folding. PLoS One 2011, 6, e20853.
-
(2011)
PLoS One
, vol.6
-
-
Coluzza, I.1
-
172
-
-
73549096657
-
Transferable coarse grain nonbonded interaction model for amino acids
-
DeVane, R.; Shinoda, W.; Moore, P.B.; Klein, M.L. Transferable coarse grain nonbonded interaction model for amino acids. J. Chem. Theory Comput. 2009, 5, 2115-2124.
-
(2009)
J. Chem. Theory Comput.
, vol.5
, pp. 2115-2124
-
-
Devane, R.1
Shinoda, W.2
Moore, P.B.3
Klein, M.L.4
-
173
-
-
58149250463
-
Toward a coarse-grained protein model coupled with a coarse-grained solvent model: Solvation free energies of amino acid side chains
-
Han, W.; Wan, C.K.; Wu, Y.D. Toward a coarse-grained protein model coupled with a coarse-grained solvent model: Solvation free energies of amino acid side chains. J. Chem. Theory Comput. 2008, 4, 1891-1901.
-
(2008)
J. Chem. Theory Comput.
, vol.4
, pp. 1891-1901
-
-
Han, W.1
Wan, C.K.2
Wu, Y.D.3
-
174
-
-
34548020295
-
A coarse-grained protein-protein potential derived from an all-atom force field
-
Basdevant, N.; Borgis, D.; Ha-Duong, T. A coarse-grained protein-protein potential derived from an all-atom force field. J. Phys. Chem. B 2007, 111, 9390-9399.
-
(2007)
J. Phys. Chem. B
, vol.111
, pp. 9390-9399
-
-
Basdevant, N.1
Borgis, D.2
Ha-Duong, T.3
-
175
-
-
33644893631
-
Coarse grained protein-lipid model with application to lipoprotein particles
-
Shih, A.Y.; Arkhipov, A.; Freddolino, P.L.; Schulten, K. Coarse grained protein-lipid model with application to lipoprotein particles. J. Phys. Chem. B 2006, 110, 3674-3684.
-
(2006)
J. Phys. Chem. B
, vol.110
, pp. 3674-3684
-
-
Shih, A.Y.1
Arkhipov, A.2
Freddolino, P.L.3
Schulten, K.4
-
176
-
-
61449085669
-
Application of Residue-Based and Shape-Based Coarse-Graining to Biomolecular Simulations
-
CRC Press: Boca Raton, FL, USA
-
Freddolino, P.L.; Shih, A.Y.; Arkhipov, A.; Ying, Y.; Chen, Z.; Schulten, K. Application of Residue-Based and Shape-Based Coarse-Graining to Biomolecular Simulations. In Coarse-Graining of Condensed Phase and Biomolecular Systems; CRC Press: Boca Raton, FL, USA, 2009; p. 299.
-
(2009)
In Coarse-Graining of Condensed Phase and Biomolecular Systems
, pp. 299
-
-
Freddolino, P.L.1
Shih, A.Y.2
Arkhipov, A.3
Ying, Y.4
Chen, Z.5
Schulten, K.6
-
177
-
-
84859175189
-
Structural basis of membrane bending by the N-BAR protein endophilin
-
Mim, C.; Cui, H.; Gawronski-Salerno, J.; Frost, A.; Lyman, E.; Voth, G.; Unger, V. Structural basis of membrane bending by the N-BAR protein endophilin. Cell 2012, 149, 137-145.
-
(2012)
Cell
, vol.149
, pp. 137-145
-
-
Mim, C.1
Cui, H.2
Gawronski-Salerno, J.3
Frost, A.4
Lyman, E.5
Voth, G.6
Unger, V.7
-
178
-
-
84872148441
-
Hybrid approach for highly coarse-grained lipid bilayer models
-
Srivastava, A.; Voth, G.A. Hybrid approach for highly coarse-grained lipid bilayer models. J. Chem. Theory Comput. 2012, 9, 750-765.
-
(2012)
J. Chem. Theory Comput.
, vol.9
, pp. 750-765
-
-
Srivastava, A.1
Voth, G.A.2
-
179
-
-
77951212412
-
PRIMO/PRIMONA: A coarse-grained model for proteins and nucleic acids that preserves near-atomistic accuracy
-
Gopal, S.M.; Mukherjee, S.; Cheng, Y.M.; Feig, M. PRIMO/PRIMONA: A coarse-grained model for proteins and nucleic acids that preserves near-atomistic accuracy. Proteins 2010, 78, 1266-1281.
-
(2010)
Proteins
, vol.78
, pp. 1266-1281
-
-
Gopal, S.M.1
Mukherjee, S.2
Cheng, Y.M.3
Feig, M.4
-
180
-
-
0020997912
-
Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
-
Kabsch, W.; Sander, C. Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983, 22, 2577-2637.
-
(1983)
Biopolymers
, vol.22
, pp. 2577-2637
-
-
Kabsch, W.1
Sander, C.2
-
181
-
-
49449113010
-
The MARTINI coarse-grained force field: Extension to proteins
-
Monticelli, L.; Kandasamy, S.K.; Periole, X.; Larson, R.G.; Tieleman, D.P.; Marrink, S.J. The MARTINI coarse-grained force field: Extension to proteins. J. Chem. Theory Comput. 2008, 4, 819-834.
-
(2008)
J. Chem. Theory Comput.
, vol.4
, pp. 819-834
-
-
Monticelli, L.1
Kandasamy, S.K.2
Periole, X.3
Larson, R.G.4
Tieleman, D.P.5
Marrink, S.J.6
-
182
-
-
33845280446
-
Comparing the polarities of the amino acids: Side-chain distribution coefficients between the vapor phase, cyclohexane, 1-octanol, and neutral aqueous solution
-
Radzicka, A.;Wolfenden, R. Comparing the polarities of the amino acids: Side-chain distribution coefficients between the vapor phase, cyclohexane, 1-octanol, and neutral aqueous solution. Biochemistry 1988, 27, 1664-1670.
-
(1988)
Biochemistry
, vol.27
, pp. 1664-1670
-
-
Radzicka, A.1
Olfenden, R.2
-
183
-
-
0019883174
-
Affinities of amino acid side chains for solvent water
-
Wolfenden, R.; Andersson, L.; Cullis, P.M.; Southgate, C.C.B. Affinities of amino acid side chains for solvent water. Biochemistry 1981, 20, 849-855.
-
(1981)
Biochemistry
, vol.20
, pp. 849-855
-
-
Wolfenden, R.1
Andersson, L.2
Cullis, P.M.3
Southgate, C.C.B.4
-
184
-
-
84872142909
-
Improved parameters for the martini coarse-grained protein force field
-
De Jong, D.H.; Singh, G.; Bennett, W.F.D.; Arnarez, C.; Wassenaar, T.A.; Schäfer, L.V.; Periole, X.; Tieleman, D.P.; Marrink, S.J. Improved parameters for the martini coarse-grained protein force field. J. Chem. Theory Comput. 2012, 9, 687-697.
-
(2012)
J. Chem. Theory Comput.
, vol.9
, pp. 687-697
-
-
De Jong, D.H.1
Singh, G.2
Bennett, W.F.D.3
Arnarez, C.4
Wassenaar, T.A.5
Schäfer, L.V.6
Periole, X.7
Tieleman, D.P.8
Marrink, S.J.9
-
185
-
-
52949088587
-
Statistically optimal analysis of samples from multiple equilibrium states
-
124105:1-124105:10
-
Shirts, M.; Chodera, J. Statistically optimal analysis of samples from multiple equilibrium states. J. Chem. Phys. 2008, 129, 124105:1-124105:10.
-
(2008)
J. Chem. Phys.
, vol.129
-
-
Shirts, M.1
Chodera, J.2
-
186
-
-
84986519238
-
The weighted histogram analysis method for free-energy calculations on biomolecules
-
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)
I. The method. 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
-
187
-
-
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
-
188
-
-
79960209915
-
Using the wimley-white hydrophobicity scale as a direct quantitative test of force fields: The MARTINI coarse-grained model
-
Singh, G.; Tieleman, D.P. Using the wimley-white hydrophobicity scale as a direct quantitative test of force fields: The MARTINI coarse-grained model. J. Chem. Theory Comput. 2011, 7, 2316-2324.
-
(2011)
J. Chem. Theory Comput.
, vol.7
, pp. 2316-2324
-
-
Singh, G.1
Tieleman, D.P.2
-
189
-
-
0029738872
-
Experimentally determined hydrophobicity scale for proteins at membrane interfaces
-
Wimley, W.C.; White, S.H. Experimentally determined hydrophobicity scale for proteins at membrane interfaces. Nat. Struct. Mol. Biol. 1996, 3, 842-848.
-
(1996)
Nat. Struct. Mol. Biol.
, vol.3
, pp. 842-848
-
-
Wimley, W.C.1
White, S.H.2
-
190
-
-
84858300656
-
Dimerization of amino acid side chains: Lessons from the comparison of different force fields
-
De Jong, D.H.; Periole, X.; Marrink, S.J. Dimerization of amino acid side chains: Lessons from the comparison of different force fields. J. Chem. Theory Comput. 2012, 8, 1003-1014.
-
(2012)
J. Chem. Theory Comput.
, vol.8
, pp. 1003-1014
-
-
De Jong, D.H.1
Periole, X.2
Marrink, S.J.3
-
191
-
-
0029919190
-
Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading
-
Miyazawa, S.; Jernigan, R.L. Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading. J. Mol. Biol. 1996, 256, 623-644.
-
(1996)
J. Mol. Biol.
, vol.256
, pp. 623-644
-
-
Miyazawa, S.1
Jernigan, R.L.2
-
192
-
-
84860708896
-
Improving internal peptide dynamics in the coarse-grained MARTINI model: Toward large-scale simulations of amyloid- and elastin-like peptides
-
Seo, M.; Rauscher, S.; Pomès, R.; Tieleman, D.P. Improving internal peptide dynamics in the coarse-grained MARTINI model: Toward large-scale simulations of amyloid- and elastin-like peptides. J. Chem. Theory Comput. 2012, 8, 1774-1785.
-
(2012)
J. Chem. Theory Comput.
, vol.8
, pp. 1774-1785
-
-
Seo, M.1
Rauscher, S.2
Pomès, R.3
Tieleman, D.P.4
-
193
-
-
4444293963
-
Simulation of domain formation in mixed DLPC-DSPC bilayers
-
Faller, R.; Marrink, S.J. Simulation of domain formation in mixed DLPC-DSPC bilayers. Langmuir 2004, 20, 7686-7693.
-
(2004)
Langmuir
, vol.20
, pp. 7686-7693
-
-
Faller, R.1
Marrink, S.J.2
-
194
-
-
0028362193
-
Structural dimensions and their changes in a reentrant hexagonal-lamellar transition of phospholipids
-
Rand, R.; Fuller, N. Structural dimensions and their changes in a reentrant hexagonal-lamellar transition of phospholipids. Biophys. J. 1994, 66, 2127-2138.
-
(1994)
Biophys. J.
, vol.66
, pp. 2127-2138
-
-
Rand, R.1
Fuller, N.2
-
195
-
-
0038661344
-
New phases of phospholipids and implications to the membrane fusion problem
-
Yang, L.; Ding, L.; Huang, H.W. New phases of phospholipids and implications to the membrane fusion problem. Biochemistry 2003, 42, 6631-6635.
-
(2003)
Biochemistry
, vol.42
, pp. 6631-6635
-
-
Yang, L.1
Ding, L.2
Huang, H.W.3
-
196
-
-
10044296377
-
Molecular view of hexagonal phase formation in phospholipid membranes
-
Marrink, S.J.; Mark, A.E. Molecular view of hexagonal phase formation in phospholipid membranes. Biophys. J. 2004, 87, 3894-3900.
-
(2004)
Biophys. J.
, vol.87
, pp. 3894-3900
-
-
Marrink, S.J.1
Mark, A.E.2
-
197
-
-
19744367689
-
Simulation of gel phase formation and melting in lipid bilayers using a coarse grained model
-
Marrink, S.J.; Risselada, 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, J.2
Mark, A.E.3
-
198
-
-
33750523614
-
Pressure-jump X-ray studies of liquid crystal transitions in lipids
-
Seddon, J.M.; Squires, A.M.; Conn, C.E.; Ces, O.; Heron, A.J.; Mulet, X.; Shearman, G.C.; Templer, R.H. Pressure-jump X-ray studies of liquid crystal transitions in lipids. Philos. Trans. R. Soc. Lond. A 2006, 364, 2635-2655.
-
(2006)
Philos. Trans. R. Soc. Lond. A
, vol.364
, pp. 2635-2655
-
-
Seddon, J.M.1
Squires, A.M.2
Conn, C.E.3
Ces, O.4
Heron, A.J.5
Mulet, X.6
Shearman, G.C.7
Templer, R.H.8
-
199
-
-
78650112488
-
Partitioning of lipids at domain boundaries in model membranes
-
Schäfer, L.V.; Marrink, S.J. Partitioning of lipids at domain boundaries in model membranes. Biophys. J. 2010, 99, L91-L93.
-
(2010)
Biophys. J.
, vol.99
-
-
Schäfer, L.V.1
Marrink, S.J.2
-
200
-
-
77749298088
-
On the antibacterial action of cyclic peptides: Insights from coarse-grained MD simulations
-
Khalfa, A.; Tarek, M. On the antibacterial action of cyclic peptides: Insights from coarse-grained MD simulations. J. Phys. Chem. B 2010, 114, 2676-2684.
-
(2010)
J. Phys. Chem. B
, vol.114
, pp. 2676-2684
-
-
Khalfa, A.1
Tarek, M.2
-
201
-
-
77958463973
-
Antimicrobial peptides induce growth of phosphatidylglycerol domains in a model bacterial membrane
-
Polyansky, A.A.; Ramaswamy, R.; Volynsky, P.E.; Sbalzarini, I.F.; Marrink, S.J.; Efremov, R.G. Antimicrobial peptides induce growth of phosphatidylglycerol domains in a model bacterial membrane. J. Phys. Chem. Lett. 2010, 1, 3108-3111.
-
(2010)
J. Phys. Chem. Lett.
, vol.1
, pp. 3108-3111
-
-
Polyansky, A.A.1
Ramaswamy, R.2
Volynsky, P.E.3
Sbalzarini, I.F.4
Marrink, S.J.5
Efremov, R.G.6
-
202
-
-
33747064957
-
Ensemble molecular dynamics yields submillisecond kinetics and intermediates of membrane fusion
-
Kasson, P.M.; Kelley, N.W.; Singhal, N.; Vrljic, M.; Brunger, A.T.; Pande, V.S. Ensemble molecular dynamics yields submillisecond kinetics and intermediates of membrane fusion. Proc. Natl. Acad. Sci. USA 2006, 103, 11916-11921.
-
(2006)
Proc. Natl. Acad. Sci. USA
, vol.103
, pp. 11916-11921
-
-
Kasson, P.M.1
Kelley, N.W.2
Singhal, N.3
Vrljic, M.4
Brunger, A.T.5
Pande, V.S.6
-
203
-
-
0042193019
-
The mechanism of vesicle fusion as revealed by molecular dynamics simulations
-
Marrink, S.J.; Mark, A.E. The mechanism of vesicle fusion as revealed by molecular dynamics simulations. J. Am. Chem. Soc. 2003, 125, 11144-11145.
-
(2003)
J. Am. Chem. Soc.
, vol.125
, pp. 11144-11145
-
-
Marrink, S.J.1
Mark, A.E.2
-
204
-
-
77952395696
-
Solvent-exposed tails as prestalk transition states for membrane fusion at low hydration
-
Smirnova, Y.G.; Marrink, S.J.; Lipowsky, R.; Knecht, V. Solvent-exposed tails as prestalk transition states for membrane fusion at low hydration. J. Am. Chem. Soc. 2010, 132, 6710-6718.
-
(2010)
J. Am. Chem. Soc.
, vol.132
, pp. 6710-6718
-
-
Smirnova, Y.G.1
Marrink, S.J.2
Lipowsky, R.3
Knecht, V.4
-
205
-
-
77954658153
-
1-25 and SP-C studied via coarse-grained molecular dynamics simulations
-
1-25 and SP-C studied via coarse-grained molecular dynamics simulations. Biochim. Biophys. Acta Biomembr. 2010, 1798, 1632-1650.
-
(2010)
Biochim. Biophys. Acta Biomembr.
, vol.1798
, pp. 1632-1650
-
-
Duncan, S.L.1
Larson, R.G.2
-
206
-
-
77956685950
-
DNA lipoplexes: Formation of the inverse hexagonal phase observed by coarse-grained molecular dynamics simulation
-
Corsi, J.; Hawtin, R.W.; Ces, O.; Attard, G.S.; Khalid, S. DNA lipoplexes: Formation of the inverse hexagonal phase observed by coarse-grained molecular dynamics simulation. Langmuir 2010, 26, 12119-12125.
-
(2010)
Langmuir
, vol.26
, pp. 12119-12125
-
-
Corsi, J.1
Hawtin, R.W.2
Ces, O.3
Attard, G.S.4
Khalid, S.5
-
207
-
-
80052550711
-
Raft registration across bilayers in a molecularly detailed model
-
Pantano, D.A.; Moore, P.B.; Klein, M.L.; Discher, D.E. Raft registration across bilayers in a molecularly detailed model. Soft Matter 2011, 7, 8182-8191.
-
(2011)
Soft Matter
, vol.7
, pp. 8182-8191
-
-
Pantano, D.A.1
Moore, P.B.2
Klein, M.L.3
Discher, D.E.4
-
208
-
-
56249119219
-
The molecular face of lipid rafts in model membranes
-
Risselada, H.J.; Marrink, S.J. The molecular face of lipid rafts in model membranes. Proc. Natl. Acad. Sci. USA 2008, 105, 17367-17372.
-
(2008)
Proc. Natl. Acad. Sci. USA
, vol.105
, pp. 17367-17372
-
-
Risselada, H.J.1
Marrink, S.J.2
-
209
-
-
27244452976
-
Tunable generic model for fluid bilayer membranes
-
011506:1-011506:4
-
Cooke, I.R.; Kremer, K.; Deserno, M. Tunable generic model for fluid bilayer membranes. Phys. Rev. E 2005, 72, 011506:1-011506:4.
-
(2005)
Phys. Rev. E
, vol.72
-
-
Cooke, I.R.1
Kremer, K.2
Deserno, M.3
-
210
-
-
34249325178
-
Aggregation and vesiculation of membrane proteins by curvature-mediated interactions
-
Reynwar, B.J.; Illya, G.; Harmandaris, V.A.; Muller, M.M.; Kremer, K.; Deserno, M. Aggregation and vesiculation of membrane proteins by curvature-mediated interactions. Nature 2007, 447, 461-464.
-
(2007)
Nature
, vol.447
, pp. 461-464
-
-
Reynwar, B.J.1
Illya, G.2
Harmandaris, V.A.3
Muller, M.M.4
Kremer, K.5
Deserno, M.6
-
211
-
-
29944444169
-
Implicit solvent simulation models for biomembranes
-
Brannigan, G.; Lin, L.L.; Brown, F. Implicit solvent simulation models for biomembranes. Eur. Biophys. J. 2006, 35, 104-124.
-
(2006)
Eur. Biophys. J.
, vol.35
, pp. 104-124
-
-
Brannigan, G.1
Lin, L.L.2
Brown, F.3
-
212
-
-
58849140540
-
Membrane-protein interactions in a generic coarse-grained model for lipid bilayers
-
West, B.; Brown, F.L.; Schmid, F. Membrane-protein interactions in a generic coarse-grained model for lipid bilayers. Biophys. J. 2009, 96, 101-115.
-
(2009)
Biophys. J.
, vol.96
, pp. 101-115
-
-
West, B.1
Brown, F.L.2
Schmid, F.3
-
213
-
-
77953056708
-
An implicit solvent coarse-grained lipid model with correct stress profile
-
205103:1-205103:8
-
Sodt, A.J.; Head-Gordon, T. An implicit solvent coarse-grained lipid model with correct stress profile. J. Chem. Phys. 2010, 132, 205103:1-205103:8.
-
(2010)
J. Chem. Phys.
, vol.132
-
-
Sodt, A.J.1
Head-Gordon, T.2
-
214
-
-
84872771577
-
Understanding the role of amphipathic helices in N-BAR domain driven membrane remodeling
-
Cui, H.; Mim, C.; Vázquez, F.; Lyman, E.; Unger, V.; Voth, G. Understanding the role of amphipathic helices in N-BAR domain driven membrane remodeling. Biophys. J. 2013, 104, 404-411.
-
(2013)
Biophys. J.
, vol.104
, pp. 404-411
-
-
Cui, H.1
Mim, C.2
Vázquez, F.3
Lyman, E.4
Unger, V.5
Voth, G.6
-
215
-
-
0037179662
-
Curvature of clathrin-coated pits driven by epsin
-
Ford, M.G.J.; Mills, I.G.; Peter, B.J.; Vallis, Y.; Praefcke, G.J.K.; Evans, P.R.; McMahon, H.T. Curvature of clathrin-coated pits driven by epsin. Nature 2002, 419, 361-366.
-
(2002)
Nature
, vol.419
, pp. 361-366
-
-
Ford, M.G.J.1
Mills, I.G.2
Peter, B.J.3
Vallis, Y.4
Praefcke, G.J.K.5
Evans, P.R.6
Mcmahon, H.T.7
-
216
-
-
33745862046
-
Membrane topology of helix 0 of the Epsin N-terminal homology domain
-
Kweon, D.; Shin, Y.; Shin, J.; Lee, J.; Lee, J.; Seo, J.; Kim, Y. Membrane topology of helix 0 of the Epsin N-terminal homology domain. Mol. Cells 2006, 21, 428-435.
-
(2006)
Mol. Cells
, vol.21
, pp. 428-435
-
-
Kweon, D.1
Shin, Y.2
Shin, J.3
Lee, J.4
Lee, J.5
Seo, J.6
Kim, Y.7
-
217
-
-
84867571103
-
Membrane binding and self-association of the epsin n-terminal homology domain
-
Lai, C.L.; Jao, C.C.; Lyman, E.; Gallop, J.L.; Peter, B.J.; McMahon, H.T.; Langen, R.; Voth, G.A. Membrane binding and self-association of the epsin n-terminal homology domain. J. Mol. Biol. 2012, 423, 800-817.
-
(2012)
J. Mol. Biol.
, vol.423
, pp. 800-817
-
-
Lai, C.L.1
Jao, C.C.2
Lyman, E.3
Gallop, J.L.4
Peter, B.J.5
Mcmahon, H.T.6
Langen, R.7
Voth, G.A.8
-
218
-
-
84856763447
-
α-synuclein induces both positive mean curvature and negative gaussian curvature in membranes
-
Braun, A.R.; Sevcsik, E.; Chin, P.; Rhoades, E.; Tristram-Nagle, S.; Sachs, J.N. α-synuclein induces both positive mean curvature and negative gaussian curvature in membranes. J. Am. Chem. Soc. 2012, 134, 2613-2620.
-
(2012)
J. Am. Chem. Soc.
, vol.134
, pp. 2613-2620
-
-
Braun, A.R.1
Sevcsik, E.2
Chin, P.3
Rhoades, E.4
Tristram-Nagle, S.5
Sachs, J.N.6
-
219
-
-
79953740665
-
Thermodynamics and mechanics of membrane curvature generation and sensing by proteins and lipids
-
Baumgart, T.; Capraro, B.R.; Zhu, C.; Das, S.L. Thermodynamics and mechanics of membrane curvature generation and sensing by proteins and lipids. Annu. Rev. Phys. Chem. 2011, 62, 483-506.
-
(2011)
Annu. Rev. Phys. Chem.
, vol.62
, pp. 483-506
-
-
Baumgart, T.1
Capraro, B.R.2
Zhu, C.3
Das, S.L.4
-
220
-
-
4544258996
-
Computational approaches to nanobiotechnology: Probing the interaction of synthetic molecules with phospholipid bilayers via a coarse grain model
-
doi:101088/0957-4484/15/9/030
-
Srinivas, G.; Klein, M.L. Computational approaches to nanobiotechnology: Probing the interaction of synthetic molecules with phospholipid bilayers via a coarse grain model. Nanotechnology 2004, 15, doi:10.1088/0957-4484/15/9/030.
-
(2004)
Nanotechnology
, vol.15
-
-
Srinivas, G.1
Klein, M.L.2
-
221
-
-
13444295344
-
α-to-inverted phase transition using coarse-grain molecular dynamics
-
α-to-inverted phase transition using coarse-grain molecular dynamics. Biophys. J. 2004, 87, 2107-2115.
-
(2004)
Biophys. J.
, vol.87
, pp. 2107-2115
-
-
Nielsen, S.O.1
Lopez, C.F.2
Ivanov, I.3
Moore, P.B.4
Shelley, J.C.5
Klein, M.L.6
-
222
-
-
22244472946
-
Lipid bilayer perturbations around a transmembrane nanotube: A coarse grain molecular dynamics study
-
Nielsen, S.O.; Ensing, B.; Ortiz, V.; Moore, P.B.; Klein, M.L. Lipid bilayer perturbations around a transmembrane nanotube: A coarse grain molecular dynamics study. Biophys. J. 2005, 88, 3822-3828.
-
(2005)
Biophys. J.
, vol.88
, pp. 3822-3828
-
-
Nielsen, S.O.1
Ensing, B.2
Ortiz, V.3
Moore, P.B.4
Klein, M.L.5
-
223
-
-
84862162535
-
Molecular simulation of hydrophobin adsorption at an oil-water interface
-
Cheung, D.L. Molecular simulation of hydrophobin adsorption at an oil-water interface. Langmuir 2012, 28, 8730-8736.
-
(2012)
Langmuir
, vol.28
, pp. 8730-8736
-
-
Cheung, D.L.1
-
224
-
-
77956579453
-
Influence of hydrophobic mismatch and amino acid composition on the lateral diffusion of transmembrane peptides
-
Ramadurai, S.; Holt, A.; Schäfer, L.V.; Krasnikov, V.V.; Rijkers, D.T.; Marrink, S.J.; Killian, J.A.; Poolman, B. Influence of hydrophobic mismatch and amino acid composition on the lateral diffusion of transmembrane peptides. Biophys. J. 2010, 99, 1447-1454.
-
(2010)
Biophys. J.
, vol.99
, pp. 1447-1454
-
-
Ramadurai, S.1
Holt, A.2
Schäfer, L.V.3
Krasnikov, V.V.4
Rijkers, D.T.5
Marrink, S.J.6
Killian, J.A.7
Poolman, B.8
-
225
-
-
78349258978
-
Multiscale computer simulation of the immature HIV-1 virion
-
Ayton, G.S.; Voth, G.A. Multiscale computer simulation of the immature HIV-1 virion. Biophys. J. 2010, 99, 2757-2765.
-
(2010)
Biophys. J.
, vol.99
, pp. 2757-2765
-
-
Ayton, G.S.1
Voth, G.A.2
-
226
-
-
50349098382
-
Molecular simulations of lipid-mediated protein-protein interactions
-
De Meyer, F.J.M.; Venturoli, M.; Smit, B. Molecular simulations of lipid-mediated protein-protein interactions. Biophys. J. 2008, 95, 1851-1865.
-
(2008)
Biophys. J.
, vol.95
, pp. 1851-1865
-
-
De Meyer, F.J.M.1
Venturoli, M.2
Smit, B.3
-
227
-
-
78649833557
-
Molecular simulation of the effect of cholesterol on lipid-mediated protein-protein interactions
-
De Meyer, F.J.M.; Rodgers, J.M.; Willems, T.F.; Smit, B. Molecular simulation of the effect of cholesterol on lipid-mediated protein-protein interactions. Biophys. J. 2010, 99, 3629-3638.
-
(2010)
Biophys. J.
, vol.99
, pp. 3629-3638
-
-
De Meyer, F.J.M.1
Rodgers, J.M.2
Willems, T.F.3
Smit, B.4
-
228
-
-
45949109759
-
Gating motions in voltage-gated potassium channels revealed by coarse-grained molecular dynamics simulations
-
Treptow, W.; Marrink, S.J.; Tarek, M. Gating motions in voltage-gated potassium channels revealed by coarse-grained molecular dynamics simulations. J. Phys. Chem. B 2008, 112, 3277-3282.
-
(2008)
J. Phys. Chem. B
, vol.112
, pp. 3277-3282
-
-
Treptow, W.1
Marrink, S.J.2
Tarek, M.3
-
229
-
-
54549113500
-
Blocking of carbon nanotube based nanoinjectors by lipids: A simulation study
-
Wallace, E.J.; Sansom, M.S.P. Blocking of carbon nanotube based nanoinjectors by lipids: A simulation study. Nano Lett. 2008, 8, 2751-2756.
-
(2008)
Nano Lett.
, vol.8
, pp. 2751-2756
-
-
Wallace, E.J.1
Sansom, M.S.P.2
-
230
-
-
44949255411
-
Computer simulation study of fullerene translocation through lipid membranes
-
Wong-Ekkabut, J.; Baoukina, S.; Triampo, W.; Tang, I.M.; Tieleman, D.P.; Monticelli, L. Computer simulation study of fullerene translocation through lipid membranes. Nat. Nano 2008, 3, 363-368.
-
(2008)
Nat. Nano
, vol.3
, pp. 363-368
-
-
Wong-Ekkabut, J.1
Baoukina, S.2
Triampo, W.3
Tang, I.M.4
Tieleman, D.P.5
Monticelli, L.6
-
231
-
-
34547998576
-
Coarse-grained simulations of ABA amphiphilic triblock copolymer solutions in thin films
-
Hatakeyama, M.; Faller, R. Coarse-grained simulations of ABA amphiphilic triblock copolymer solutions in thin films. Phys. Chem. Chem. Phys. 2007, 9, 4662-4672.
-
(2007)
Phys. Chem. Chem. Phys.
, vol.9
, pp. 4662-4672
-
-
Hatakeyama, M.1
Faller, R.2
-
232
-
-
33749607009
-
Molecular dynamics simulations of PAMAM dendrimer-induced pore formation in DPPC bilayers with a coarse-grained model
-
Lee, H.; Larson, R.G. Molecular dynamics simulations of PAMAM dendrimer-induced pore formation in DPPC bilayers with a coarse-grained model. J. Phys. Chem. B 2006, 110, 18204-18211.
-
(2006)
J. Phys. Chem. B
, vol.110
, pp. 18204-18211
-
-
Lee, H.1
Larson, R.G.2
-
233
-
-
47749142781
-
Coarse-grained molecular dynamics studies of the concentration and size dependence of fifth- and seventh-generation PAMAM dendrimers on pore formation in DMPC bilayer
-
Lee, H.; Larson, R.G. Coarse-grained molecular dynamics studies of the concentration and size dependence of fifth- and seventh-generation PAMAM dendrimers on pore formation in DMPC bilayer. J. Phys. Chem. B 2008, 112, 7778-7784.
-
(2008)
J. Phys. Chem. B
, vol.112
, pp. 7778-7784
-
-
Lee, H.1
Larson, R.G.2
-
234
-
-
54249159300
-
Lipid bilayer curvature and pore formation induced by charged linear polymers and dendrimers: The effect of molecular shape
-
Lee, H.; Larson, R.G. Lipid bilayer curvature and pore formation induced by charged linear polymers and dendrimers: The effect of molecular shape. J. Phys. Chem. B 2008, 112, 12279-12285.
-
(2008)
J. Phys. Chem. B
, vol.112
, pp. 12279-12285
-
-
Lee, H.1
Larson, R.G.2
-
235
-
-
34548146523
-
G protein-coupled receptors self-assemble in dynamics simulations of model bilayers
-
Periole, X.; Huber, T.; Marrink, S.J.; Sakmar, T.P. G protein-coupled receptors self-assemble in dynamics simulations of model bilayers. J. Am. Chem. Soc. 2007, 129, 10126-10132.
-
(2007)
J. Am. Chem. Soc.
, vol.129
, pp. 10126-10132
-
-
Periole, X.1
Huber, T.2
Marrink, S.J.3
Sakmar, T.P.4
-
236
-
-
33644644163
-
Insertion and assembly of membrane proteins via simulation
-
Bond, P.J.; Sansom, M.S.P. Insertion and assembly of membrane proteins via simulation. J. Am. Chem. Soc. 2006, 128, 2697-2704.
-
(2006)
J. Am. Chem. Soc.
, vol.128
, pp. 2697-2704
-
-
Bond, P.J.1
Sansom, M.S.P.2
-
237
-
-
53249150686
-
Coarse-grained molecular dynamics simulations of the energetics of helix insertion into a lipid bilayer
-
Bond, P.J.; Wee, C.L.; Sansom, M.S.P. Coarse-grained molecular dynamics simulations of the energetics of helix insertion into a lipid bilayer. Biochemistry 2008, 47, 11321-11331.
-
(2008)
Biochemistry
, vol.47
, pp. 11321-11331
-
-
Bond, P.J.1
Wee, C.L.2
Sansom, M.S.P.3
-
238
-
-
49549088809
-
Association energetics of membrane spanning α-helices
-
MacKenzie, K.R.; Fleming, K.G. Association energetics of membrane spanning α-helices. Curr. Opin. Struct. Biol. 2008, 18, 412-419.
-
(2008)
Curr. Opin. Struct. Biol.
, vol.18
, pp. 412-419
-
-
Mackenzie, K.R.1
Fleming, K.G.2
-
239
-
-
78349243645
-
Role of lipids in spheroidal high density lipoproteins
-
e1000964
-
Vuorela, T.; Catte, A.; Niemelä, P.S.; Hall, A.; Hyvönen, M.T.; Marrink, S.J.; Karttunen, M.; Vattulainen, I. Role of lipids in spheroidal high density lipoproteins. PLoS Comput. Biol. 2010, 6, e1000964.
-
(2010)
PLoS Comput. Biol.
, vol.6
-
-
Vuorela, T.1
Catte, A.2
Niemelä, P.S.3
Hall, A.4
Hyvönen, M.T.5
Marrink, S.J.6
Karttunen, M.7
Vattulainen, I.8
-
240
-
-
28844494903
-
Coarse-grained model of proteins incorporating atomistic detail of the active site
-
218102:1-218102:4
-
Neri, M.; Anselmi, C.; Cascella, M.; Maritan, A.; Carloni, P. Coarse-grained model of proteins incorporating atomistic detail of the active site. Phys. Rev. Lett. 2005, 95, 218102:1-218102:4.
-
(2005)
Phys. Rev. Lett.
, vol.95
-
-
Neri, M.1
Anselmi, C.2
Cascella, M.3
Maritan, A.4
Carloni, P.5
-
241
-
-
33645277151
-
Molecular dynamics simulations of outer-membrane protease T from E
-
doi:101088/0953-8984/18/14/S16
-
Neri, M.; Anselmi, C.; Carnevale, V.; Vargiu, A.V.; Carloni, P. Molecular dynamics simulations of outer-membrane protease T from E. coli based on a hybrid coarse-grained/atomistic potential. J. Phys. Condens. Matter 2006, 18, doi:10.1088/0953-8984/18/14/S16.
-
(2006)
coli based on a hybrid coarse-grained/atomistic potential. J. Phys. Condens. Matter
, vol.18
-
-
Neri, M.1
Anselmi, C.2
Carnevale, V.3
Vargiu, A.V.4
Carloni, P.5
-
242
-
-
84867684737
-
Hybrid molecular mechanics/coarse-grained simulations for structural prediction of G-protein coupled receptor/ligand complexes
-
Leguèbe, M.; Nguyen, C.; Capece, L.; Hoang, Z.; Giorgetti, A.; Carloni, P. Hybrid molecular mechanics/coarse-grained simulations for structural prediction of G-protein coupled receptor/ligand complexes. PLoS One 2012, 7, e47332.
-
(2012)
PLoS One
, vol.7
-
-
Leguèbe, M.1
Nguyen, C.2
Capece, L.3
Hoang, Z.4
Giorgetti, A.5
Carloni, P.6
-
243
-
-
0034521981
-
Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models
-
Kollman, P.A.; Massova, I.; Reyes, C.; Kuhn, B.; Huo, S.; Chong, L.; Lee, M.; Lee, T.; Duan, Y.; Wang, W.; et al. Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models. Acc. Chem. Res. 2000, 33, 889-897.
-
(2000)
Acc. Chem. Res.
, vol.33
, pp. 889-897
-
-
Kollman, P.A.1
Massova, I.2
Reyes, C.3
Kuhn, B.4
Huo, S.5
Chong, L.6
Lee, M.7
Lee, T.8
Duan, Y.9
Wang, W.10
-
244
-
-
18744403982
-
Interfacial folding and membrane insertion of designed peptides studied by molecular dynamics simulations
-
Im, W.; Brooks, C.L. Interfacial folding and membrane insertion of designed peptides studied by molecular dynamics simulations. Proc. Natl. Acad. Sci. USA 2005, 102, 6771-6776.
-
(2005)
Proc. Natl. Acad. Sci. USA
, vol.102
, pp. 6771-6776
-
-
Im, W.1
Brooks, C.L.2
-
245
-
-
79959749835
-
Hybrid simulations: Combining atomistic and coarse-grained force fields using virtual sites
-
Rzepiela, A.J.; Louhivuori, M.; Peter, C.; Marrink, S.J. Hybrid simulations: Combining atomistic and coarse-grained force fields using virtual sites. Phys. Chem. Chem. Phys. 2011, 13, 10437-10448.
-
(2011)
Phys. Chem. Chem. Phys.
, vol.13
, pp. 10437-10448
-
-
Rzepiela, A.J.1
Louhivuori, M.2
Peter, C.3
Marrink, S.J.4
-
246
-
-
0030735760
-
Configurations of fluid membranes and vesicles
-
Seifert, U. Configurations of fluid membranes and vesicles. Adv. Phys. 1997, 46, 13-137.
-
(1997)
Adv. Phys.
, vol.46
, pp. 13-137
-
-
Seifert, U.1
-
247
-
-
0022098530
-
Effect of thermal undulations on the rigidity of fluid membranes and interfaces
-
Helfrich, W. Effect of thermal undulations on the rigidity of fluid membranes and interfaces. J. Phys. Fr. 1985, 46, 1263-1268.
-
(1985)
J. Phys. Fr.
, vol.46
, pp. 1263-1268
-
-
Helfrich, W.1
-
248
-
-
33744740021
-
On the scale dependence, due to thermal fluctuations, of the elastic properties of membranes
-
Föster, D. On the scale dependence, due to thermal fluctuations, of the elastic properties of membranes. Phys. Lett. A 1986, 114, 115-120.
-
(1986)
Phys. Lett. A
, vol.114
, pp. 115-120
-
-
Föster, D.1
-
249
-
-
33646127615
-
A consistent model for thermal fluctuations and protein-induced deformations in lipid bilayers
-
Brannigan, G.; Brown, F.L. A consistent model for thermal fluctuations and protein-induced deformations in lipid bilayers. Biophys. J. 2006, 90, 1501-1520.
-
(2006)
Biophys. J.
, vol.90
, pp. 1501-1520
-
-
Brannigan, G.1
Brown, F.L.2
-
250
-
-
51349132613
-
Mechanosensitive channels: Insights from continuum-based simulations
-
Tang, Y.; Yoo, J.; Yethiraj, A.; Cui, Q.; Chen, X. Mechanosensitive channels: Insights from continuum-based simulations. Cell Biochem. Biophys. 2008, 52, 1-18.
-
(2008)
Cell Biochem. Biophys.
, vol.52
, pp. 1-18
-
-
Tang, Y.1
Yoo, J.2
Yethiraj, A.3
Cui, Q.4
Chen, X.5
-
251
-
-
36049017896
-
A second generation mesoscopic lipid bilayer model: Connections to field-theory descriptions of membranes and nonlocal hydrodynamics
-
064906:1-064906:12
-
Ayton, G.S.; McWhirter, J.L.; Voth, G.A. A second generation mesoscopic lipid bilayer model: Connections to field-theory descriptions of membranes and nonlocal hydrodynamics. J. Chem. Phys. 2006, 124, 064906:1-064906:12.
-
(2006)
J. Chem. Phys.
, vol.124
-
-
Ayton, G.S.1
Mcwhirter, J.L.2
Voth, G.A.3
-
252
-
-
22244446431
-
Coupling field theory with continuum mechanics: A simulation of domain formation in giant unilamellar vesicles
-
Ayton, G.S.; McWhirter, J.L.; McMurtry, P.; Voth, G.A. Coupling field theory with continuum mechanics: A simulation of domain formation in giant unilamellar vesicles. Biophys. J. 2005, 88, 3855-3869.
-
(2005)
Biophys. J.
, vol.88
, pp. 3855-3869
-
-
Ayton, G.S.1
Mcwhirter, J.L.2
Mcmurtry, P.3
Voth, G.A.4
-
253
-
-
34548090976
-
Multiscale coupling of mesoscopic-and atomistic-level lipid bilayer simulations
-
244716:1-244716:12
-
Chang, R.; Ayton, G.S.; Voth, G.A. Multiscale coupling of mesoscopic-and atomistic-level lipid bilayer simulations. J. Chem. Phys. 2005, 122, 244716:1-244716:12.
-
(2005)
J. Chem. Phys.
, vol.122
-
-
Chang, R.1
Ayton, G.S.2
Voth, G.A.3
-
254
-
-
68949086190
-
Calculation of free energies in fluid membranes subject to heterogeneous curvature fields
-
011925:1-011925:8
-
Agrawal, N.J.; Radhakrishnan, R. Calculation of free energies in fluid membranes subject to heterogeneous curvature fields. Phys. Rev. E 2009, 80, 011925:1-011925:8.
-
(2009)
Phys. Rev. E
, vol.80
-
-
Agrawal, N.J.1
Radhakrishnan, R.2
-
255
-
-
78049436709
-
Minimal mesoscale model for protein-mediated vesiculation in clathrin-dependent endocytosis
-
Agrawal, N.J.; Nukpezah, J.; Radhakrishnan, R. Minimal mesoscale model for protein-mediated vesiculation in clathrin-dependent endocytosis. PLoS Comput. Biol. 2010, 6, e1000926.
-
(2010)
PLoS Comput. Biol.
, vol.6
-
-
Agrawal, N.J.1
Nukpezah, J.2
Radhakrishnan, R.3
-
256
-
-
84862530752
-
Mesoscale simulations of curvature-inducing protein partitioning on lipid bilayer membranes in the presence of mean curvature fields
-
Liu, J.; Tourdot, R.; Ramanan, V.; Agrawal, N.J.; Radhakrishanan, R. Mesoscale simulations of curvature-inducing protein partitioning on lipid bilayer membranes in the presence of mean curvature fields. Mol. Phys. 2012, 110, 1127-1137.
-
(2012)
Mol. Phys.
, vol.110
, pp. 1127-1137
-
-
Liu, J.1
Tourdot, R.2
Ramanan, V.3
Agrawal, N.J.4
Radhakrishanan, R.5
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