-
1
-
-
0037120092
-
Coarse-graining in polymer simulation: From the atomistic to the mesoscopic scale and back
-
Muller-Plathe, F. 2002. Coarse-graining in polymer simulation: from the atomistic to the mesoscopic scale and back. ChemPhysChem. 3:755-769.
-
(2002)
ChemPhysChem
, vol.3
, pp. 755-769
-
-
Muller-Plathe, F.1
-
2
-
-
0035846402
-
Simulations of phospholipids using a coarse grain model
-
Shelley, J. C., M. Y. Shelley, R. C. Reeder, S. Bandyopadhyay, P. B. Moore, and M. L. Klein. 2001. Simulations of phospholipids using a coarse grain model. J. Phys. Chem. B. 105:9785-9792.
-
(2001)
J. Phys. Chem. B
, vol.105
, pp. 9785-9792
-
-
Shelley, J.C.1
Shelley, M.Y.2
Reeder, R.C.3
Bandyopadhyay, S.4
Moore, P.B.5
Klein, M.L.6
-
3
-
-
0345098288
-
Molecular dynamics simulation of the formation, structure, and dynamics of small phospholipid vesicles
-
Marrink, S. J., and A. E. Mark. 2003. Molecular dynamics simulation of the formation, structure, and dynamics of small phospholipid vesicles. J. Am. Chem. Soc. 125:15233-15242.
-
(2003)
J. Am. Chem. Soc
, vol.125
, pp. 15233-15242
-
-
Marrink, S.J.1
Mark, A.E.2
-
4
-
-
0036783398
-
Folding and stretching in a Go-like model of titin
-
Cieplak, M., T. X. Hoang, and M. O. Robbins. 2002. Folding and stretching in a Go-like model of titin. Proteins. 49:114-124.
-
(2002)
Proteins
, vol.49
, pp. 114-124
-
-
Cieplak, M.1
Hoang, T.X.2
Robbins, M.O.3
-
5
-
-
85035231429
-
Effective pair potentials between protein amino acids
-
Pliego-Pastrana, P., and M. D. Carbajal-Tinoco. 2003. Effective pair potentials between protein amino acids. Phys. Rev. E. 68:011903.
-
(2003)
Phys. Rev. E
, vol.68
, pp. 011903
-
-
Pliego-Pastrana, P.1
Carbajal-Tinoco, M.D.2
-
6
-
-
1842454935
-
Orientational potentials extracted from protein structures improve native fold recognition
-
Buchete, N. V., J. E. Straub, and D. Thirumalai. 2004. Orientational potentials extracted from protein structures improve native fold recognition. Protein Sci. 13:862-874.
-
(2004)
Protein Sci
, vol.13
, pp. 862-874
-
-
Buchete, N.V.1
Straub, J.E.2
Thirumalai, D.3
-
7
-
-
17044393884
-
Coarse-grained models for proteins
-
Tozzini, V. 2005. Coarse-grained models for proteins. Curr. Opin. Struct. Biol. 15:144-150.
-
(2005)
Curr. Opin. Struct. Biol
, vol.15
, pp. 144-150
-
-
Tozzini, V.1
-
8
-
-
0019569599
-
Noninteracting local-structure model of folding and unfolding transition in globular proteins
-
Go, N., and H. Abe. 1981. Noninteracting local-structure model of folding and unfolding transition in globular proteins. I. Formulation. Biopolymers. 20:991-1011.
-
(1981)
I. Formulation. Biopolymers
, vol.20
, pp. 991-1011
-
-
Go, N.1
Abe, H.2
-
9
-
-
34548105157
-
Monte Carlo simulations of polyalanine using a reduced model and statistics-based interaction potentials
-
van Giessen, A. E., and J. E. Straub. 2005. Monte Carlo simulations of polyalanine using a reduced model and statistics-based interaction potentials. J. Chem. Phys. 122:024904.
-
(2005)
J. Chem. Phys
, vol.122
, pp. 024904
-
-
van Giessen, A.E.1
Straub, J.E.2
-
10
-
-
0035424584
-
Cumulant-based expressions for the multibody terms for the correlation between local and electrostatic interactions in the united-residue force field
-
Liwo, A., C. Czaplewski, J. Pillardy, and H. A. Scheraga. 2001. Cumulant-based expressions for the multibody terms for the correlation between local and electrostatic interactions in the united-residue force field. J. Chem. Phys. 115:2323-2347.
-
(2001)
J. Chem. Phys
, vol.115
, pp. 2323-2347
-
-
Liwo, A.1
Czaplewski, C.2
Pillardy, J.3
Scheraga, H.A.4
-
11
-
-
28944442465
-
Kinetic studies of folding of the B-domain of staphylococcal protein A with molecular dynamics and a united-residue (UNRES) model of polypeptide chains
-
Khalili, M., A. Liwo, and H. A. Scheraga. 2006. Kinetic studies of folding of the B-domain of staphylococcal protein A with molecular dynamics and a united-residue (UNRES) model of polypeptide chains. J. Mol. Biol. 355:536-547.
-
(2006)
J. Mol. Biol
, vol.355
, pp. 536-547
-
-
Khalili, M.1
Liwo, A.2
Scheraga, H.A.3
-
12
-
-
0035882537
-
Assembly of a tetrameric alpha-helical bundle: Computer simulations on an intermediate-resolution protein model
-
Smith, A. V., and C. K. Hall. 2001. Assembly of a tetrameric alpha-helical bundle: computer simulations on an intermediate-resolution protein model. Proteins. 44:376-391.
-
(2001)
Proteins
, vol.44
, pp. 376-391
-
-
Smith, A.V.1
Hall, C.K.2
-
13
-
-
17444374698
-
Mesoscale model of polymer melt structure: Self-consistent mapping of molecular correlations to coarse-grained potentials
-
Ashbaugh, H. S., H. A. Patel, S. K. Kumar, and S. Garde. 2005. Mesoscale model of polymer melt structure: self-consistent mapping of molecular correlations to coarse-grained potentials. J. Chem. Phys. 122:104908.
-
(2005)
J. Chem. Phys
, vol.122
, pp. 104908
-
-
Ashbaugh, H.S.1
Patel, H.A.2
Kumar, S.K.3
Garde, S.4
-
14
-
-
0042783950
-
Deriving effective mesoscale potentials from atomistic simulations
-
Reith, D., M. Putz, and F. Muller-Plathe. 2003. Deriving effective mesoscale potentials from atomistic simulations. J. Comput. Chem. 24:1624-1636.
-
(2003)
J. Comput. Chem
, vol.24
, pp. 1624-1636
-
-
Reith, D.1
Putz, M.2
Muller-Plathe, F.3
-
15
-
-
84940492598
-
Interatomic potentials from first-principles calculations: The force-matching method
-
Ercolessi, F., and J. Adams. 1994. Interatomic potentials from first-principles calculations: the force-matching method. Europhys. Lett. 26:583-588.
-
(1994)
Europhys. Lett
, vol.26
, pp. 583-588
-
-
Ercolessi, F.1
Adams, J.2
-
16
-
-
3042598406
-
Effective force fields for condensed phase systems from ab initio molecular dynamics simulation: A new method for force-matching
-
Izvekov, S., M. Parrinello, C. J. Burnham, and G. A. Voth. 2004. Effective force fields for condensed phase systems from ab initio molecular dynamics simulation: a new method for force-matching. J. Chem. Phys. 120:10896-10913.
-
(2004)
J. Chem. Phys
, vol.120
, pp. 10896-10913
-
-
Izvekov, S.1
Parrinello, M.2
Burnham, C.J.3
Voth, G.A.4
-
17
-
-
17444368060
-
Effective force field for liquid hydrogen fluoride from ab initio molecular dynamics simulation using the force-matching method
-
Izvekov, S., and G. A. Voth. 2005. Effective force field for liquid hydrogen fluoride from ab initio molecular dynamics simulation using the force-matching method. J. Phys. Chem. B. 109:6573-6586.
-
(2005)
J. Phys. Chem. B
, vol.109
, pp. 6573-6586
-
-
Izvekov, S.1
Voth, G.A.2
-
18
-
-
14544291957
-
A multiscale coarse-graining method for biomolecular systems
-
Izvekov, S., and G. A. Voth. 2005. A multiscale coarse-graining method for biomolecular systems. J. Phys. Chem. B. 109:2469-2473.
-
(2005)
J. Phys. Chem. B
, vol.109
, pp. 2469-2473
-
-
Izvekov, S.1
Voth, G.A.2
-
19
-
-
33644929350
-
Multiscale coarse graining of liquid-state systems
-
Izvekov, S., and G. A. Voth. 2005. Multiscale coarse graining of liquid-state systems. J. Chem. Phys. 123:134105.
-
(2005)
J. Chem. Phys
, vol.123
, pp. 134105
-
-
Izvekov, S.1
Voth, G.A.2
-
20
-
-
33748250745
-
Multiscale coarse-graining of mixed phospholipid/cholesterol bilayers
-
Izvekov, S., and G. A. Voth. 2006. Multiscale coarse-graining of mixed phospholipid/cholesterol bilayers. J. Chem. Theory Comput. 2:637-648.
-
(2006)
J. Chem. Theory Comput
, vol.2
, pp. 637-648
-
-
Izvekov, S.1
Voth, G.A.2
-
21
-
-
33644903231
-
Multiscale coarse-graining of ionic liquids
-
Wang, Y. T., S. Izvekov, T. Y. Yan, and G. A. Voth. 2006. Multiscale coarse-graining of ionic liquids. J. Phys. Chem. B. 110:3564-3575.
-
(2006)
J. Phys. Chem. B
, vol.110
, pp. 3564-3575
-
-
Wang, Y.T.1
Izvekov, S.2
Yan, T.Y.3
Voth, G.A.4
-
22
-
-
33746912421
-
A coarse-grained molecular dynamics study of carbon nanoparticle aggregation
-
Izvekov, S., and A. Violi. 2006. A coarse-grained molecular dynamics study of carbon nanoparticle aggregation. J. Chem. Theory Comput. 2:504-512.
-
(2006)
J. Chem. Theory Comput
, vol.2
, pp. 504-512
-
-
Izvekov, S.1
Violi, A.2
-
23
-
-
85030502362
-
-
MacKerell, A. D. Jr., B. Brooks, C. L. Brooks III, L. Nilsson, B. Roux, Y. Won, and M. Karplus. 1998. CHARMM: the energy function and its parameterization with an overview of the program. In The Encyclopedia of Computational Chemistry. P. v. R. Schleyer, editor. John Wiley and Sons, Chichester, UK. 271-277.
-
MacKerell, A. D. Jr., B. Brooks, C. L. Brooks III, L. Nilsson, B. Roux, Y. Won, and M. Karplus. 1998. CHARMM: the energy function and its parameterization with an overview of the program. In The Encyclopedia of Computational Chemistry. P. v. R. Schleyer, editor. John Wiley and Sons, Chichester, UK. 271-277.
-
-
-
-
24
-
-
0001767031
-
Thermodynamics and kinetics of folding of two model peptides investigated by molecular dynamics simulations
-
Ferrara, P., J. Apostolakis, and A. Caflisch. 2000. Thermodynamics and kinetics of folding of two model peptides investigated by molecular dynamics simulations. J. Phys. Chem. B. 104:5000-5010.
-
(2000)
J. Phys. Chem. B
, vol.104
, pp. 5000-5010
-
-
Ferrara, P.1
Apostolakis, J.2
Caflisch, A.3
-
25
-
-
0004016501
-
Comparison of simple potential functions for simulating liquid water
-
Jorgensen, W. L., J. Chandrasekhar, J. D. Madura, R. W. Impey, and M. L. Klein. 1983. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79:926-935.
-
(1983)
J. Chem. Phys
, vol.79
, pp. 926-935
-
-
Jorgensen, W.L.1
Chandrasekhar, J.2
Madura, J.D.3
Impey, R.W.4
Klein, M.L.5
-
26
-
-
85030503503
-
-
Smith, W., T. R. Forester, I. T. Todorov, and M. Leslie. 2006. DL_POLY. CCLRC Daresbury Laboratory, Daresbury, Warrington, UK.
-
Smith, W., T. R. Forester, I. T. Todorov, and M. Leslie. 2006. DL_POLY. CCLRC Daresbury Laboratory, Daresbury, Warrington, UK.
-
-
-
-
27
-
-
33646940952
-
Numerical integration of Cartesian equations of motion of a system with constraints: Molecular-dynamics of n-alkanes
-
Ryckaert, J. P., G. Ciccotti, and H. J. C. Berendsen. 1977. Numerical integration of Cartesian equations of motion of a system with constraints: molecular-dynamics of n-alkanes. J. Comput. Phys. 23:327-341.
-
(1977)
J. Comput. Phys
, vol.23
, pp. 327-341
-
-
Ryckaert, J.P.1
Ciccotti, G.2
Berendsen, H.J.C.3
-
28
-
-
34248359980
-
Multiscale coarse-graining and structural correlations: Connections to liquid state theory
-
In press
-
Noid, W. G., J.-W. Chu, G. S. Ayton, and G. A. Voth. 2007. Multiscale coarse-graining and structural correlations: connections to liquid state theory. J. Phys. Chem. B. In press.
-
(2007)
J. Phys. Chem. B
-
-
Noid, W.G.1
Chu, J.-W.2
Ayton, G.S.3
Voth, G.A.4
-
29
-
-
33846213672
-
Mapping allatom models onto one-bead coarse-grained models: General properties and applications to a minimal polypeptide model
-
Tozzini, V., W. Rocchia, and J. A. McCammon. 2006. Mapping allatom models onto one-bead coarse-grained models: general properties and applications to a minimal polypeptide model. J. Chem. Theory Comput. 2:667-673.
-
(2006)
J. Chem. Theory Comput
, vol.2
, pp. 667-673
-
-
Tozzini, V.1
Rocchia, W.2
McCammon, J.A.3
-
30
-
-
33750181654
-
Modeling real dynamics in the coarse-grained representation of condensed phase systems
-
Izvekov, S., and G. A. Voth. 2006. Modeling real dynamics in the coarse-grained representation of condensed phase systems. J. Chem. Phys. 125:151101.
-
(2006)
J. Chem. Phys
, vol.125
, pp. 151101
-
-
Izvekov, S.1
Voth, G.A.2
|