-
3
-
-
1442281293
-
A method for accelerating the molecular dynamics simulation of infrequent events
-
Voter A.F. A method for accelerating the molecular dynamics simulation of infrequent events. J. Chem. Phys. 1997, 106:4665-4677.
-
(1997)
J. Chem. Phys.
, vol.106
, pp. 4665-4677
-
-
Voter, A.F.1
-
4
-
-
0001208056
-
Parallel replica method for dynamics of infrequent events
-
Voter A.F. Parallel replica method for dynamics of infrequent events. Phys. Rev. B 1998, 57:13985-13988.
-
(1998)
Phys. Rev. B
, vol.57
, pp. 13985-13988
-
-
Voter, A.F.1
-
5
-
-
0033688171
-
Temperature-accelerated dynamics for simulation of infrequent events
-
Sorensen M.R., Voter A.F. Temperature-accelerated dynamics for simulation of infrequent events. J. Chem. Phys. 2000, 112:9599-9606.
-
(2000)
J. Chem. Phys.
, vol.112
, pp. 9599-9606
-
-
Sorensen, M.R.1
Voter, A.F.2
-
6
-
-
33845204189
-
Stability and dynamics of virus capsids described by coarse-graining modeling
-
Arkhipov A., Freddolino P.L., Schulten K. Stability and dynamics of virus capsids described by coarse-graining modeling. Structure 2006, 14:1767-1777.
-
(2006)
Structure
, vol.14
, pp. 1767-1777
-
-
Arkhipov, A.1
Freddolino, P.L.2
Schulten, K.3
-
9
-
-
0016610491
-
Computer simulation of protein folding
-
Levitt M., Warshel A. Computer simulation of protein folding. Nature 1975, 253:694-698.
-
(1975)
Nature
, vol.253
, pp. 694-698
-
-
Levitt, M.1
Warshel, A.2
-
10
-
-
0017157584
-
A simplified representation of protein conformations for rapid simulation of protein folding
-
Levitt M. A simplified representation of protein conformations for rapid simulation of protein folding. J. Mol. Biol. 1976, 104:59-107.
-
(1976)
J. Mol. Biol.
, vol.104
, pp. 59-107
-
-
Levitt, M.1
-
11
-
-
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
-
12
-
-
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
-
13
-
-
0001022293
-
On the role of hydrodynamic interactions in block copolymer microphase separation
-
Groot R.D., Madden T.J., Tildesley D.J.J. On the role of hydrodynamic interactions in block copolymer microphase separation. J. Chem. Phys. 1999, 110:9739-9749.
-
(1999)
J. Chem. Phys.
, vol.110
, pp. 9739-9749
-
-
Groot, R.D.1
Madden, T.J.2
Tildesley, D.J.J.3
-
14
-
-
0035902367
-
A coarse grain model for phospholipid simulations
-
Shelley J.C., Shelley M.Y., Reeder R.C., Bandyopadhyay C., 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, C.4
Klein, M.L.5
-
15
-
-
0037120092
-
Coarse-graining in polymer simulation: From the atomistic to the mesoscopic scale and back
-
Muller-Plathe F. Coarse-graining in polymer simulation: From the atomistic to the mesoscopic scale and back. Chem. Phys. Chem. 2002, 3:754.
-
(2002)
Chem. Phys. Chem.
, vol.3
, pp. 754
-
-
Muller-Plathe, F.1
-
16
-
-
0037449387
-
A coarse-grained model for particle dynamics simulations of complex fiuids
-
Liew C.C., Mikami M. A coarse-grained model for particle dynamics simulations of complex fiuids. Chem. Phys. Lett. 2003, 368:346-351.
-
(2003)
Chem. Phys. Lett.
, vol.368
, pp. 346-351
-
-
Liew, C.C.1
Mikami, M.2
-
17
-
-
0037455730
-
Computer simulations for macromolecular science
-
Kremer K. Computer simulations for macromolecular science. Macromol. Chem. Phys. 2003, 204:257-264.
-
(2003)
Macromol. Chem. Phys.
, vol.204
, pp. 257-264
-
-
Kremer, K.1
-
18
-
-
0142198916
-
A coarse grain model for n-alkanes parameterized from surface tension data
-
Nelsen S.O., Lopex C.F., Srinivas G., Klein M.L. A coarse grain model for n-alkanes parameterized from surface tension data. J. Chem. Phys. 2003, 204:7043-7049.
-
(2003)
J. Chem. Phys.
, vol.204
, pp. 7043-7049
-
-
Nelsen, S.O.1
Lopex, C.F.2
Srinivas, G.3
Klein, M.L.4
-
19
-
-
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
-
20
-
-
27744486126
-
Mechanical properties of surfactant bilayer membranes from atomistic and coarse-grained molecular dynamics simulations
-
Boek E.S., Padding T.J., den Otter W.K., Briels W.J. Mechanical properties of surfactant bilayer membranes from atomistic and coarse-grained molecular dynamics simulations. J. Phys. Chem. B 2005, 109:19851-19858.
-
(2005)
J. Phys. Chem. B
, vol.109
, pp. 19851-19858
-
-
Boek, E.S.1
Padding, T.J.2
den Otter, W.K.3
Briels, W.J.4
-
21
-
-
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
-
22
-
-
33847198330
-
Multiscale simulation of transmembrane proteins
-
Ayton G.S., Voth G.A. Multiscale simulation of transmembrane proteins. J. Struct. Biol. 2007, 157:570-578.
-
(2007)
J. Struct. Biol.
, vol.157
, pp. 570-578
-
-
Ayton, G.S.1
Voth, G.A.2
-
23
-
-
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
-
24
-
-
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
-
25
-
-
33947408324
-
Multi-property fitting and parameterization of a coarse grained model for aqueous surfactants
-
Shinoda W., Devane R., Klein M.L. Multi-property fitting and parameterization of a coarse grained model for aqueous surfactants. Mol. Simul. 2007, 33:27-36.
-
(2007)
Mol. Simul.
, vol.33
, pp. 27-36
-
-
Shinoda, W.1
Devane, R.2
Klein, M.L.3
-
26
-
-
34548809141
-
A coarse-grained protein force field for folding and structure prediction
-
Maupetit J., Tuffery P., Derreumaux P. A coarse-grained protein force field for folding and structure prediction. Proteins 2007, 69:394-408.
-
(2007)
Proteins
, vol.69
, pp. 394-408
-
-
Maupetit, J.1
Tuffery, P.2
Derreumaux, P.3
-
27
-
-
46149109506
-
The multiscale coarse-graining method. I. A rigorous bridge between atomistic and coarse-grained models
-
Noid W., Chu J.W., Ayton G.S., Izvekov S., Voth G.A., Das A., Andersen H.C. The multiscale coarse-graining method. I. A rigorous bridge between atomistic and coarse-grained models. J. Chem. Phys. 2008, 128:244114.
-
(2008)
J. Chem. Phys.
, vol.128
, pp. 244114
-
-
Noid, W.1
Chu, J.W.2
Ayton, G.S.3
Izvekov, S.4
Voth, G.A.5
Das, A.6
Andersen, H.C.7
-
28
-
-
46149099398
-
The multiscale coarse-graining method. II. Numerical implementation for coarse-grained molecular models
-
Noid W., Liu P., Wang Y., Chu J.W., Izvekov S., Andersen H.C., Voth G.A. The multiscale coarse-graining method. II. Numerical implementation for coarse-grained molecular models. J. Chem. Phys. 2008, 128:244115.
-
(2008)
J. Chem. Phys.
, vol.128
, pp. 244115
-
-
Noid, W.1
Liu, P.2
Wang, Y.3
Chu, J.W.4
Izvekov, S.5
Andersen, H.C.6
Voth, G.A.7
-
29
-
-
37549009571
-
Coarse-grained models for simulations of multiprotein complexes: Application to ubiquitin binding
-
Kim Y.C., Hummer G. Coarse-grained models for simulations of multiprotein complexes: Application to ubiquitin binding. J. Mol. Biol. 2008, 375:1416-1433.
-
(2008)
J. Mol. Biol.
, vol.375
, pp. 1416-1433
-
-
Kim, Y.C.1
Hummer, G.2
-
30
-
-
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
-
31
-
-
41149141988
-
Classical simulations from the atomistic to the mesoscale: Coarse graining an azobenzene liquid crystal
-
Peter C., Site D.L., Kremer K. Classical simulations from the atomistic to the mesoscale: Coarse graining an azobenzene liquid crystal. Soft Matter 2008, 4:859.
-
(2008)
Soft Matter
, vol.4
, pp. 859
-
-
Peter, C.1
Site, D.L.2
Kremer, K.3
-
32
-
-
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 2009, 78:1266-1281.
-
(2009)
Proteins
, vol.78
, pp. 1266-1281
-
-
Gopal, S.M.1
Mukherjee, S.2
Cheng, Y.M.3
Feig, M.4
-
33
-
-
70349458094
-
A force field for virtual atom molecular mechanics of proteins
-
Korkut A., Hendrickson W.A. A force field for virtual atom molecular mechanics of proteins. Proc. Natl. Acad. Sci. U.S.A. 2009, 106:15667-15672.
-
(2009)
Proc. Natl. Acad. Sci. U.S.A.
, vol.106
, pp. 15667-15672
-
-
Korkut, A.1
Hendrickson, W.A.2
-
34
-
-
77950149115
-
Efficient, regularized, and scalable algorithms for multi-scale coarse-graining
-
Lu L., Izvekov S., Das A., Andersen H.C., Voth G.A. Efficient, regularized, and scalable algorithms for multi-scale coarse-graining. J. Chem. Theory Comput. 2010, 6:954-965.
-
(2010)
J. Chem. Theory Comput.
, vol.6
, pp. 954-965
-
-
Lu, L.1
Izvekov, S.2
Das, A.3
Andersen, H.C.4
Voth, G.A.5
-
35
-
-
78651240463
-
A coarse-grained model of DNA with explicit solvation by water and ions
-
DeMille R.C., Cheatham T.E., Molinero V. A coarse-grained model of DNA with explicit solvation by water and ions. J. Phys. Chem. B 2011, 115:132-142.
-
(2011)
J. Phys. Chem. B
, vol.115
, pp. 132-142
-
-
DeMille, R.C.1
Cheatham, T.E.2
Molinero, V.3
-
36
-
-
79251480753
-
Coarse-grained dynamics of protein synthesis in a cell-free system
-
Karzbrun E., Shin J., Bar-Ziz R.H., Noireaux V. Coarse-grained dynamics of protein synthesis in a cell-free system. Phys. Rev. Lett. 2011, 106:048104.
-
(2011)
Phys. Rev. Lett.
, vol.106
, pp. 048104
-
-
Karzbrun, E.1
Shin, J.2
Bar-Ziz, R.H.3
Noireaux, V.4
-
37
-
-
79952606527
-
A coarse-grained model for molecular dynamics simulations of native cellulose
-
Wohlert J., Berglund L.A. A coarse-grained model for molecular dynamics simulations of native cellulose. J. Chem. Theory Comput. 2011, 73:753-760.
-
(2011)
J. Chem. Theory Comput.
, vol.73
, pp. 753-760
-
-
Wohlert, J.1
Berglund, L.A.2
-
38
-
-
0035420584
-
Many-body interactions and correlations in coarse-grained descriptions of polymer solutions
-
Bolhuis P.G., Louis A.A., Hansen J.P. Many-body interactions and correlations in coarse-grained descriptions of polymer solutions. Phys. Rev. E 2001, 64:021801.
-
(2001)
Phys. Rev. E
, vol.64
, pp. 021801
-
-
Bolhuis, P.G.1
Louis, A.A.2
Hansen, J.P.3
-
39
-
-
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
-
40
-
-
33644929350
-
Multiscale coarse-graining of liquid state systems
-
Izvekov S., Voth G.A. Multiscale coarse-graining of liquid state systems. J. Chem. Phys. 2005, 123:134105.
-
(2005)
J. Chem. Phys.
, vol.123
, pp. 134105
-
-
Izvekov, S.1
Voth, G.A.2
-
41
-
-
34347230979
-
Equation of motion for coarse-grained simulation based on microscopic description
-
Kinjo T., Hyodo S. Equation of motion for coarse-grained simulation based on microscopic description. Phys. Rev. E 2007, 75:051109.
-
(2007)
Phys. Rev. E
, vol.75
, pp. 051109
-
-
Kinjo, T.1
Hyodo, S.2
-
42
-
-
77950250945
-
A generalized Yvon-Born-Green theory for determining coarse-grained interaction potentials
-
Mullinax J.W., Noid W. A generalized Yvon-Born-Green theory for determining coarse-grained interaction potentials. J. Phys. Chem. C 2010, 114:5661-5674.
-
(2010)
J. Phys. Chem. C
, vol.114
, pp. 5661-5674
-
-
Mullinax, J.W.1
Noid, W.2
-
43
-
-
79951893060
-
An improved coarse-grained model of solvation and the hydrophobic effect
-
Varilly P., Patel A.J., Chandler D. An improved coarse-grained model of solvation and the hydrophobic effect. J. Chem. Phys. 2011, 134:074109.
-
(2011)
J. Chem. Phys.
, vol.134
, pp. 074109
-
-
Varilly, P.1
Patel, A.J.2
Chandler, D.3
-
44
-
-
1942420790
-
Application of coarse grained models to the analysis of macromolecular structures
-
Lattanzi G. Application of coarse grained models to the analysis of macromolecular structures. Comput. Mater. Sci. 2004, 30:163-171.
-
(2004)
Comput. Mater. Sci.
, vol.30
, pp. 163-171
-
-
Lattanzi, G.1
-
45
-
-
17044393884
-
Coarse-grained models for proteins
-
Tozzini V. Coarse-grained models for proteins. Curr. Opin. Struct. Biol. 2005, 15:144-150.
-
(2005)
Curr. Opin. Struct. Biol.
, vol.15
, pp. 144-150
-
-
Tozzini, V.1
-
46
-
-
37349066472
-
Special section of multiscale modeling in biology
-
Schlick T., Dill K. Special section of multiscale modeling in biology. Multiscale Model. Simul. 2006, 5:1174.
-
(2006)
Multiscale Model. Simul.
, vol.5
, pp. 1174
-
-
Schlick, T.1
Dill, K.2
-
48
-
-
43049121037
-
Theoretical models for bridging timescales in polymer dynamics
-
Guenza M.G. Theoretical models for bridging timescales in polymer dynamics. J. Phys. Condens. Matter 2008, 20:033101.
-
(2008)
J. Phys. Condens. Matter
, vol.20
, pp. 033101
-
-
Guenza, M.G.1
-
49
-
-
41049093757
-
Multiscale simulation of soft matter: From scale bridging to adaptive resolution
-
Praprotnik M., Site D.L., Kremer K. Multiscale simulation of soft matter: From scale bridging to adaptive resolution. Annu. Rev. Phys. Chem. 2008, 59:545.
-
(2008)
Annu. Rev. Phys. Chem.
, vol.59
, pp. 545
-
-
Praprotnik, M.1
Site, D.L.2
Kremer, K.3
-
50
-
-
64749106745
-
Systematic multiscale simulation of membrane protein systems
-
Ayton G.S., Voth G.A. Systematic multiscale simulation of membrane protein systems. Curr. Opin. Struct. Biol. 2009, 19:138-144.
-
(2009)
Curr. Opin. Struct. Biol.
, vol.19
, pp. 138-144
-
-
Ayton, G.S.1
Voth, G.A.2
-
51
-
-
67650586561
-
Multiscale modeling of polymer materials using field-theoretic methodologies: A survey about recent developments
-
Baeurle S.A. Multiscale modeling of polymer materials using field-theoretic methodologies: A survey about recent developments. J. Math. Chem. 2009, 46:363.
-
(2009)
J. Math. Chem.
, vol.46
, pp. 363
-
-
Baeurle, S.A.1
-
52
-
-
67349249092
-
Coarse-grained modeling of lipids
-
Bennum S.V., Hoopes M.I., Xing C.Y., Faller R. Coarse-grained modeling of lipids. Chem. Phys. Lipids 2009, 159:59.
-
(2009)
Chem. Phys. Lipids
, vol.159
, pp. 59
-
-
Bennum, S.V.1
Hoopes, M.I.2
Xing, C.Y.3
Faller, R.4
-
53
-
-
77954958041
-
Review of hierarchical multiscale modeling to describe the mechanical behavior of amorphous polymers
-
Bouvard J.L., Ward D.K., Hossain D., Nouranian S., Marin E.B., Horstemeyer M.F. Review of hierarchical multiscale modeling to describe the mechanical behavior of amorphous polymers. J. Eng. Mater. Technol. 2009, 131:041206.
-
(2009)
J. Eng. Mater. Technol.
, vol.131
, pp. 041206
-
-
Bouvard, J.L.1
Ward, D.K.2
Hossain, D.3
Nouranian, S.4
Marin, E.B.5
Horstemeyer, M.F.6
-
54
-
-
71749118247
-
Theoretically informed coarse grain simulations of block copolymer melts: Method and applications
-
Detcheverry F.A., Pike D.Q., Nagpal U., Nealey P.F., de Pablo J.J. Theoretically informed coarse grain simulations of block copolymer melts: Method and applications. Soft Matter 2009, 5:4858.
-
(2009)
Soft Matter
, vol.5
, pp. 4858
-
-
Detcheverry, F.A.1
Pike, D.Q.2
Nagpal, U.3
Nealey, P.F.4
de Pablo, J.J.5
-
55
-
-
63449129633
-
Insights from coarse-grained Go models for protein folding and dynamics
-
Hills R.D., Brooks C.L. Insights from coarse-grained Go models for protein folding and dynamics. Int. J. Mol. Sci. 2009, 10:889.
-
(2009)
Int. J. Mol. Sci.
, vol.10
, pp. 889
-
-
Hills, R.D.1
Brooks, C.L.2
-
56
-
-
62349124337
-
Multiscale modeling of emergent materials: Biological and soft matter
-
Murtola T., Bunker A., Vattulainen I., Deserno M., Karttunen M. Multiscale modeling of emergent materials: Biological and soft matter. Phys. Chem. Chem. Phys. 2009, 11:1869.
-
(2009)
Phys. Chem. Chem. Phys.
, vol.11
, pp. 1869
-
-
Murtola, T.1
Bunker, A.2
Vattulainen, I.3
Deserno, M.4
Karttunen, M.5
-
57
-
-
77954826956
-
Molecular dynamics simulations of glassy polymers
-
Barrat J.L., Baschnagel J., Lyulin A. Molecular dynamics simulations of glassy polymers. Soft Matter 2010, 6:3430.
-
(2010)
Soft Matter
, vol.6
, pp. 3430
-
-
Barrat, J.L.1
Baschnagel, J.2
Lyulin, A.3
-
58
-
-
78149461723
-
Coarse-grained models to study dynamics of nanoscale biomolecules and their applications to the ribosome
-
Trylksa J. Coarse-grained models to study dynamics of nanoscale biomolecules and their applications to the ribosome. J. Phys. Condens. Matter 2010, 22:453101-453114.
-
(2010)
J. Phys. Condens. Matter
, vol.22
, pp. 453101-453114
-
-
Trylksa, J.1
-
59
-
-
79953762337
-
Coarse-grained simulations of macromolecules: From DNA to nanocomposites
-
de Pablo J.J. Coarse-grained simulations of macromolecules: From DNA to nanocomposites. Annu. Rev. Phys. Chem. 2011, 62:555.
-
(2011)
Annu. Rev. Phys. Chem.
, vol.62
, pp. 555
-
-
de Pablo, J.J.1
-
60
-
-
79953742584
-
Coarse-grained (multiscale) simulations in studies of biophysical and chemical systems
-
Kamerlin S., Vicatos S., Dryga A., Warshel A. Coarse-grained (multiscale) simulations in studies of biophysical and chemical systems. Annu. Rev. Phys. Chem. 2011, 62:41-64.
-
(2011)
Annu. Rev. Phys. Chem.
, vol.62
, pp. 41-64
-
-
Kamerlin, S.1
Vicatos, S.2
Dryga, A.3
Warshel, A.4
-
61
-
-
79953081933
-
Coarse-grained models for protein aggregations
-
Wu C., Shea J.E. Coarse-grained models for protein aggregations. Curr. Opin. Struct. Biol. 2011, 21:209-220.
-
(2011)
Curr. Opin. Struct. Biol.
, vol.21
, pp. 209-220
-
-
Wu, C.1
Shea, J.E.2
-
63
-
-
73949130043
-
MARTINI coarse-grained force field: Extension to carbohydrates
-
Lopez C.A., Rzepiela A.J., de Vries A.H., Dijkhuizen L., Hunenberger P.H., Marrink S.J. MARTINI coarse-grained force field: Extension to carbohydrates. J. Chem. Theory Comput. 2009, 5:3195-3210.
-
(2009)
J. Chem. Theory Comput.
, vol.5
, pp. 3195-3210
-
-
Lopez, C.A.1
Rzepiela, A.J.2
de Vries, A.H.3
Dijkhuizen, L.4
Hunenberger, P.H.5
Marrink, S.J.6
-
65
-
-
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. U.S.A. 2008, 105:17367-17372.
-
(2008)
Proc. Natl. Acad. Sci. U.S.A.
, vol.105
, pp. 17367-17372
-
-
Risselada, H.J.1
Marrink, S.J.2
-
66
-
-
77956162800
-
Cholesterol in bilayers with PUFA chains: Doping with DMPC or POPC results in sterol reorientation and membrane-domain formation
-
Kucerka N., Marquardy D., Harroun T.A., Nieh M.P., Wassall S.R., de Jong D.H., Schafer L.V., Marrink S.J., Katsaras J. Cholesterol in bilayers with PUFA chains: Doping with DMPC or POPC results in sterol reorientation and membrane-domain formation. Biochemistry 2010, 79:7485-7493.
-
(2010)
Biochemistry
, vol.79
, pp. 7485-7493
-
-
Kucerka, N.1
Marquardy, D.2
Harroun, T.A.3
Nieh, M.P.4
Wassall, S.R.5
de Jong, D.H.6
Schafer, L.V.7
Marrink, S.J.8
Katsaras, J.9
-
67
-
-
70350223830
-
Concerted diffusion of lipids in raft-like membranes
-
Apajalahti T., Niemela P., Govindan P.N., Miettinen M., Salonen E., Marrink S.J., Vattulainen I. Concerted diffusion of lipids in raft-like membranes. Faraday Discuss. 2010, 144:411-430.
-
(2010)
Faraday Discuss.
, vol.144
, pp. 411-430
-
-
Apajalahti, T.1
Niemela, P.2
Govindan, P.N.3
Miettinen, M.4
Salonen, E.5
Marrink, S.J.6
Vattulainen, I.7
-
68
-
-
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
-
69
-
-
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. 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.4
-
70
-
-
70350774221
-
Simulations of the C-subunit of the ATP-synthase reveal helix rearrangements
-
Sengupta D., Rampioni A., Marrink S.J. Simulations of the C-subunit of the ATP-synthase reveal helix rearrangements. Mol. Membr. Biol. 2009, 26:422-434.
-
(2009)
Mol. Membr. Biol.
, vol.26
, pp. 422-434
-
-
Sengupta, D.1
Rampioni, A.2
Marrink, S.J.3
-
71
-
-
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
-
72
-
-
43149103416
-
Mechanosensitive membrane channels in action
-
Yefimov S., Onck P.R., van der Giessen E., 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
Onck, P.R.2
van der Giessen, E.3
Marrink, S.J.4
-
73
-
-
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. U.S.A. 2010, 107:19856-19860.
-
(2010)
Proc. Natl. Acad. Sci. U.S.A.
, vol.107
, pp. 19856-19860
-
-
Louhivuori, M.1
Risselada, H.J.2
van der Giessen, E.3
Marrink, S.J.4
-
74
-
-
77954912142
-
Immobilization of the plug domain inside the SecY channel allows unrestricted protein translocation
-
Lycklama a Nijeholt J.A., 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
-
-
Lycklama a Nijeholt, J.A.1
Bulacu, M.2
Marrink, S.J.3
Driessen, A.J.M.4
-
75
-
-
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
-
76
-
-
4444293963
-
Simulation of domain formation in DLPC-DSPC mixed bilayers
-
Faller R., Marrink S.J. Simulation of domain formation in DLPC-DSPC mixed bilayers. Langmuir 2004, 20:7686-7693.
-
(2004)
Langmuir
, vol.20
, pp. 7686-7693
-
-
Faller, R.1
Marrink, S.J.2
-
77
-
-
19744367689
-
Simulation of gel phase formation and melting in lipid bilayers using a coarse grained model
-
Marrink S.J., Risselada H.J., Mark A.E. Simulation of gel phase formation and melting in lipid bilayers using a coarse grained model. Chem. Phys. Lipids 2005, 135:223-244.
-
(2005)
Chem. Phys. Lipids
, vol.135
, pp. 223-244
-
-
Marrink, S.J.1
Risselada, H.J.2
Mark, A.E.3
-
78
-
-
38349032639
-
Cholesterol shows preference for the interior of polyunsaturated lipid membranes
-
Marrink S.J., de Vries A.H., Harroun T.A., Katsaras J., Wassall S.R. Cholesterol shows preference for the interior of polyunsaturated lipid membranes. J. Am. Chem. Soc. 2008, 130:10-11.
-
(2008)
J. Am. Chem. Soc.
, vol.130
, pp. 10-11
-
-
Marrink, S.J.1
de Vries, A.H.2
Harroun, T.A.3
Katsaras, J.4
Wassall, S.R.5
-
79
-
-
69349085157
-
A molecular view of cholesterol fiip-fiop and chemical potential in different membrane environments
-
Bennett W.F.D., MacCallum J.L., Hinner M.J., Marrink S.J., Tieleman D.P. A molecular view of cholesterol fiip-fiop and chemical potential in different membrane environments. J. Am. Chem. Soc. 2009, 131:12714-12720.
-
(2009)
J. Am. Chem. Soc.
, vol.131
, pp. 12714-12720
-
-
Bennett, W.F.D.1
MacCallum, J.L.2
Hinner, M.J.3
Marrink, S.J.4
Tieleman, D.P.5
-
80
-
-
72149121112
-
Location, tilt, and binding: A molecular dynamics study of voltage-sensitive dyes in biomembranes
-
Hinner M.J., Marrink S.J., de Vries A.H. Location, tilt, and binding: A molecular dynamics study of voltage-sensitive dyes in biomembranes. J. Phys. Chem. B 2009, 113:15807-15819.
-
(2009)
J. Phys. Chem. B
, vol.113
, pp. 15807-15819
-
-
Hinner, M.J.1
Marrink, S.J.2
de Vries, A.H.3
-
81
-
-
44049107643
-
Structure of spheroidal HDL particles revealed by combined atomistic and coarse grained simulations
-
Catte A., Patterson J.C., Bashtovyy D., Jones M.K., Gu F., Li L., Rampioni A., Sengupta D., Vuorela T., Niemela P., Karttunen M., Marrink S.J., Vattulainen I., Segrest J.P. Structure of spheroidal HDL particles revealed by combined atomistic and coarse grained simulations. Biophys. J. 2008, 94:2306-2319.
-
(2008)
Biophys. J.
, vol.94
, pp. 2306-2319
-
-
Catte, A.1
Patterson, J.C.2
Bashtovyy, D.3
Jones, M.K.4
Gu, F.5
Li, L.6
Rampioni, A.7
Sengupta, D.8
Vuorela, T.9
Niemela, P.10
Karttunen, M.11
Marrink, S.J.12
Vattulainen, I.13
Segrest, J.P.14
-
82
-
-
78349243645
-
Role of lipids in spheroidal high density lipoproteins
-
Vuorela T., Catte A., Niemela P., Hall A., Hyvonen 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
Niemela, P.3
Hall, A.4
Hyvonen, M.T.5
Marrink, S.J.6
Karttunen, M.7
Vattulainen, I.8
-
83
-
-
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. Chem. Phys. Chem. 2007, 8:452-461.
-
(2007)
Chem. Phys. Chem.
, 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
-
84
-
-
84946450438
-
Algorithms for macromolecular dynamics and constraint dynamics
-
van Gunsteren W.F., Berendsen H.J.C. Algorithms for macromolecular dynamics and constraint dynamics. Mol. Phys. 1977, 34:1311-1327.
-
(1977)
Mol. Phys.
, vol.34
, pp. 1311-1327
-
-
van Gunsteren, W.F.1
Berendsen, H.J.C.2
-
85
-
-
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
-
86
-
-
62349116492
-
On using a too large integration time step in molecular dynamics simulations of coarse-grained molecular models
-
Winger M., Trzesniak D., Baron R., van Gunsteren W.F. On using a too large integration time step in molecular dynamics simulations of coarse-grained molecular models. Phys. Chem. Chem. Phys. 2009, 11:1934-1941.
-
(2009)
Phys. Chem. Chem. Phys.
, vol.11
, pp. 1934-1941
-
-
Winger, M.1
Trzesniak, D.2
Baron, R.3
van Gunsteren, W.F.4
-
87
-
-
77149124571
-
Comment on "on using a too large integration time step in molecular dynamics simulations of coarse-grained molecular models" by M. Winger, D. Trzesniak, R. Baron and W.F. van Gunsteren, Phys. Chem. Chem. Phys., 2009, 11, 1934
-
Marrink S.J., Periole X., Tieleman D.P., de Vries A.H. Comment on "on using a too large integration time step in molecular dynamics simulations of coarse-grained molecular models" by M. Winger, D. Trzesniak, R. Baron and W.F. van Gunsteren, Phys. Chem. Chem. Phys., 2009, 11, 1934. Phys. Chem. Chem. Phys. 2010, 12:2254.
-
(2010)
Phys. Chem. Chem. Phys.
, vol.12
, pp. 2254
-
-
Marrink, S.J.1
Periole, X.2
Tieleman, D.P.3
de Vries, A.H.4
-
88
-
-
77149125910
-
Reply to the 'comment on "on using a too large integration time step in molecular dynamics simulations of coarse-grained molecular models"' by S.J. Marrink, X. Periole, D. Peter Tieleman and Alex H. de Vries, Phys. Chem. Chem. Phys., 2010, 12, doi: 10.1039/b915293h
-
van Gunsteren W.F., Winger M. Reply to the 'comment on "on using a too large integration time step in molecular dynamics simulations of coarse-grained molecular models"' by S.J. Marrink, X. Periole, D. Peter Tieleman and Alex H. de Vries, Phys. Chem. Chem. Phys., 2010, 12, doi: 10.1039/b915293h. Phys. Chem. Chem. Phys. 2010, 12:2257.
-
(2010)
Phys. Chem. Chem. Phys.
, vol.12
, pp. 2257
-
-
van Gunsteren, W.F.1
Winger, M.2
-
89
-
-
27344436659
-
Scalable molecular dynamics with NAMD
-
Phillips J.C., Braun R., Wang W., Gumbart J., Tajkorshid E., Villa E., Chipot C., Skeel R.D., Kale 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
Tajkorshid, E.5
Villa, E.6
Chipot, C.7
Skeel, R.D.8
Kale, L.9
Schulten, K.10
-
91
-
-
33847193915
-
Assembly of lipoproteins particles revealed by coarse-grained molecular dynamics simulations
-
Shih A.Y., Freddolino P.L., Arkhipov A., Schulten K. Assembly of lipoproteins 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
-
92
-
-
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
-
93
-
-
33845381177
-
Coarse-grained molecular dynamics simulations of a rotating bacterial flagellum
-
Arkhipov A., Freddolino P.L., Imada K., Namba K., Schulten K. Coarse-grained molecular dynamics simulations of a rotating bacterial flagellum. Biophys. J. 2006, 91:4589-4597.
-
(2006)
Biophys. J.
, vol.91
, pp. 4589-4597
-
-
Arkhipov, A.1
Freddolino, P.L.2
Imada, K.3
Namba, K.4
Schulten, K.5
-
94
-
-
0028204732
-
Topology-representing networks
-
Martinetz T., Schulten K. Topology-representing networks. Neural Netw. 1994, 7:507-522.
-
(1994)
Neural Netw.
, vol.7
, pp. 507-522
-
-
Martinetz, T.1
Schulten, K.2
-
95
-
-
0041784950
-
All-atom empirical potential for molecular modeling and dynamics studies of proteins
-
MacKerell A.D., Bashford D., Bellott M., Dunbrack R.L., Evanseck J., Field M.J., Fischer S., Gao J., Guo H., Ha S., Joseph D., Kuchnir L. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B 1998, 102:3586-3616.
-
(1998)
J. Phys. Chem. B
, vol.102
, pp. 3586-3616
-
-
MacKerell, A.D.1
Bashford, D.2
Bellott, M.3
Dunbrack, R.L.4
Evanseck, J.5
Field, M.J.6
Fischer, S.7
Gao, J.8
Guo, H.9
Ha, S.10
Joseph, D.11
Kuchnir, L.12
-
96
-
-
80054040379
-
-
University of Illinois at Urbana-Champaign, Urbana-Champaign, IL
-
Arkhipov A., Yin Y., Chandler D., Hsin J., Vandivort K. Shape-Based Coarse Graining Tutorial, Theoretical and Biophysics Group 2010, University of Illinois at Urbana-Champaign, Urbana-Champaign, IL, http://www.ks.uiuc.edu/Training/Tutorials/science/coarse-graining/sbcg-tutorial.pdf.
-
(2010)
Shape-Based Coarse Graining Tutorial, Theoretical and Biophysics Group
-
-
Arkhipov, A.1
Yin, Y.2
Chandler, D.3
Hsin, J.4
Vandivort, K.5
-
97
-
-
56049086620
-
Coarse-grained molecular modeling of nonionic surfactant self assembly
-
Shinoda W., Devane R., Klein M.L. Coarse-grained molecular modeling of nonionic surfactant self assembly. Soft Matter 2008, 4:2454.
-
(2008)
Soft Matter
, vol.4
, pp. 2454
-
-
Shinoda, W.1
Devane, R.2
Klein, M.L.3
-
98
-
-
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
-
99
-
-
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.
-
(2009)
J. Chem. Theory Comput.
, vol.5
, pp. 2115
-
-
Devane, R.1
Shinoda, W.2
Moore, P.B.3
Klein, M.L.4
-
100
-
-
77952478054
-
Coarse grained potential models for phenyl based molecules: I. Parametrization using experimental data
-
Devane R., Klein M.L., Chiu C., Nielsen S.O., Shinoda W., Moore P.B. Coarse grained potential models for phenyl based molecules: I. Parametrization using experimental data. J. Phys. Chem. B 2010, 114:6386.
-
(2010)
J. Phys. Chem. B
, vol.114
, pp. 6386
-
-
Devane, R.1
Klein, M.L.2
Chiu, C.3
Nielsen, S.O.4
Shinoda, W.5
Moore, P.B.6
-
101
-
-
77955495231
-
Coarse grained potential models for phenyl based molecules: II. Application to fullerenes
-
Chiu C., Devane R., Klein M.L., Shinoda W., Moore P.B., Nielsen S.O. Coarse grained potential models for phenyl based molecules: II. Application to fullerenes. J. Phys. Chem. B 2010, 114:6894.
-
(2010)
J. Phys. Chem. B
, vol.114
, pp. 6894
-
-
Chiu, C.1
Devane, R.2
Klein, M.L.3
Shinoda, W.4
Moore, P.B.5
Nielsen, S.O.6
-
102
-
-
78650145822
-
Parametrization and application of a coarse grained force field for benzene/fullerene interactions with lipids
-
Devane R., Jusufi A., Shinoda W., Chiu C.C., Nielsen S.O., Moore P.B., Klein M. Parametrization and application of a coarse grained force field for benzene/fullerene interactions with lipids. J. Phys. Chem. B 2010, 114:16364-16372.
-
(2010)
J. Phys. Chem. B
, vol.114
, pp. 16364-16372
-
-
Devane, R.1
Jusufi, A.2
Shinoda, W.3
Chiu, C.C.4
Nielsen, S.O.5
Moore, P.B.6
Klein, M.7
-
103
-
-
3042683179
-
Simulation of diblock copolymer self-assembly, using a coarse-grain model
-
Srinivas G., Shelley J.C., Nielsen S.O., Discher D.E., Klein M.L. Simulation of diblock copolymer self-assembly, using a coarse-grain model. J. Chem. Phys. 2004, 108:8153-8160.
-
(2004)
J. Chem. Phys.
, vol.108
, pp. 8153-8160
-
-
Srinivas, G.1
Shelley, J.C.2
Nielsen, S.O.3
Discher, D.E.4
Klein, M.L.5
-
104
-
-
4444346350
-
Self-assembly and properties of diblock copolymers by coarse-grain molecular dynamics
-
Srinivas G., Discher D.E., Klein M.L. Self-assembly and properties of diblock copolymers by coarse-grain molecular dynamics. Nat. Mater. 2004, 3:638-644.
-
(2004)
Nat. Mater.
, vol.3
, pp. 638-644
-
-
Srinivas, G.1
Discher, D.E.2
Klein, M.L.3
-
105
-
-
4444321604
-
Coarse-grain molecular dynamics simulations of diblock copolymer surfactants interacting with a lipid bilayer
-
Srinivas G., Klein M.L. Coarse-grain molecular dynamics simulations of diblock copolymer surfactants interacting with a lipid bilayer. Mol. Phys. 2004, 102:883-889.
-
(2004)
Mol. Phys.
, vol.102
, pp. 883-889
-
-
Srinivas, G.1
Klein, M.L.2
-
106
-
-
30644460809
-
Key roles for chain fiexibility in block copolymer membranes that contain pores or make tubes
-
Srinivas G., Discher D.E., Klein M.L. Key roles for chain fiexibility in block copolymer membranes that contain pores or make tubes. Nano Lett. 2005, 5:2343-2349.
-
(2005)
Nano Lett.
, vol.5
, pp. 2343-2349
-
-
Srinivas, G.1
Discher, D.E.2
Klein, M.L.3
-
108
-
-
0002467378
-
Fast parallel algorithms for short-range molecular dynamics
-
Plimpton S. Fast parallel algorithms for short-range molecular dynamics. J. Comput. Phys. 1995, 117:1-19.
-
(1995)
J. Comput. Phys.
, vol.117
, pp. 1-19
-
-
Plimpton, S.1
-
109
-
-
41249087856
-
General purpose molecular dynamics simulations fully implemented on graphics processing units
-
Anderson J.A., Lorenz C.D., Travesset A. General purpose molecular dynamics simulations fully implemented on graphics processing units. J. Comput. Phys. 2008, 227:5342-5359.
-
(2008)
J. Comput. Phys.
, vol.227
, pp. 5342-5359
-
-
Anderson, J.A.1
Lorenz, C.D.2
Travesset, A.3
-
110
-
-
36449001478
-
Molecular dynamics algorithm for multiple time scales: Systems with long range forces
-
Tuckerman M.E., Berene B.J., Martyna G.J. Molecular dynamics algorithm for multiple time scales: Systems with long range forces. J. Chem. Phys. 1991, 10:6811-6815.
-
(1991)
J. Chem. Phys.
, vol.10
, pp. 6811-6815
-
-
Tuckerman, M.E.1
Berene, B.J.2
Martyna, G.J.3
-
111
-
-
33746606875
-
The multiscale challenge for biomolecular systems: Coarse-grained modeling
-
Chu J.W., Izvekov S., Voth G.A. The multiscale challenge for biomolecular systems: Coarse-grained modeling. Mol. Simul. 2006, 32:211.
-
(2006)
Mol. Simul.
, vol.32
, pp. 211
-
-
Chu, J.W.1
Izvekov, S.2
Voth, G.A.3
-
112
-
-
34247098754
-
Multiscale modeling of biomolecular systems: In serial and in parallel
-
Ayton G.S., Noid W., Voth G.A. Multiscale modeling of biomolecular systems: In serial and in parallel. Curr. Opin. Struct. Biol. 2007, 17:192.
-
(2007)
Curr. Opin. Struct. Biol.
, vol.17
, pp. 192
-
-
Ayton, G.S.1
Noid, W.2
Voth, G.A.3
-
113
-
-
33947421578
-
Emerging methods for multiscale simulation of biomolecular systems
-
Chu J.W., Ayton G.S., Izvekov S., Voth G.A. Emerging methods for multiscale simulation of biomolecular systems. Mol. Phys. 2007, 105:167.
-
(2007)
Mol. Phys.
, vol.105
, pp. 167
-
-
Chu, J.W.1
Ayton, G.S.2
Izvekov, S.3
Voth, G.A.4
-
114
-
-
34248359980
-
Multiscale coarse-graining and structural correlations: Connections to liquid state theory
-
Noid W., Chu J.W., Ayton G.S., Voth G.A. Multiscale coarse-graining and structural correlations: Connections to liquid state theory. J. Phys. Chem. B 2007, 111:4116.
-
(2007)
J. Phys. Chem. B
, vol.111
, pp. 4116
-
-
Noid, W.1
Chu, J.W.2
Ayton, G.S.3
Voth, G.A.4
-
115
-
-
33847717840
-
Smart resolution replica exchange: An efficient algorithm for exploring complex energy landscapes
-
Liu P., Voth G.A. Smart resolution replica exchange: An efficient algorithm for exploring complex energy landscapes. J. Chem. Phys. 2007, 126:045106.
-
(2007)
J. Chem. Phys.
, vol.126
, pp. 045106
-
-
Liu, P.1
Voth, G.A.2
-
116
-
-
34247852583
-
Coarse-grained peptide modeling using a systematic multiscale approach
-
Zhou J., Thorpe I.F., Izvekov S., Voth G.A. Coarse-grained peptide modeling using a systematic multiscale approach. Biophys. J. 2007, 92:4289-4303.
-
(2007)
Biophys. J.
, vol.92
, pp. 4289-4303
-
-
Zhou, J.1
Thorpe, I.F.2
Izvekov, S.3
Voth, G.A.4
-
117
-
-
33748250745
-
Multiscale coarse graining of mixed phospholipid/cholesterol bilayers
-
Izvekov S., Voth G.A. Multiscale coarse graining of mixed phospholipid/cholesterol bilayers. J. Chem. Theory Comput. 2006, 2:637.
-
(2006)
J. Chem. Theory Comput.
, vol.2
, pp. 637
-
-
Izvekov, S.1
Voth, G.A.2
-
118
-
-
35348950936
-
Multiscale coarse-graining of monosaccharides
-
Liu P., Izvekov S., Voth G.A. Multiscale coarse-graining of monosaccharides. J. Phys. Chem. B 2007, 111:11566.
-
(2007)
J. Phys. Chem. B
, vol.111
, pp. 11566
-
-
Liu, P.1
Izvekov, S.2
Voth, G.A.3
-
119
-
-
33750181654
-
Modeling real dynamics in the coarse-grained representations of condensed phase systems
-
Izvekov S., Voth G.A. Modeling real dynamics in the coarse-grained representations of condensed phase systems. J. Chem. Phys. 2006, 125:151101.
-
(2006)
J. Chem. Phys.
, vol.125
, pp. 151101
-
-
Izvekov, S.1
Voth, G.A.2
-
120
-
-
24644486893
-
Unique spatial heterogeneity in ionic liquids
-
Wang Y., Voth G.A. Unique spatial heterogeneity in ionic liquids. J. Am. Chem. Soc. 2005, 127:12192.
-
(2005)
J. Am. Chem. Soc.
, vol.127
, pp. 12192
-
-
Wang, Y.1
Voth, G.A.2
-
121
-
-
33644903231
-
Multiscale coarse-graining of ionic liquids
-
Wang Y., Izvekov S., Yan T., Voth G.A. Multiscale coarse-graining of ionic liquids. J. Phys. Chem. B 2006, 110:3564.
-
(2006)
J. Phys. Chem. B
, vol.110
, pp. 3564
-
-
Wang, Y.1
Izvekov, S.2
Yan, T.3
Voth, G.A.4
-
122
-
-
65249158495
-
Transferable coarse-grained models for ionic liquids
-
Wang Y., Feng S., Voth G.A. Transferable coarse-grained models for ionic liquids. J. Chem. Theory Comput. 2009, 5:1091-1098.
-
(2009)
J. Chem. Theory Comput.
, vol.5
, pp. 1091-1098
-
-
Wang, Y.1
Feng, S.2
Voth, G.A.3
-
123
-
-
33748266722
-
Mixed atomistic and coarse-grained molecular dynamics: Simulation of a membrane-bound ion channel
-
Shi Q., Izvekov S., Voth G.A. Mixed atomistic and coarse-grained molecular dynamics: Simulation of a membrane-bound ion channel. J. Phys. Chem. B Lett. 2006, 110:15045-15048.
-
(2006)
J. Phys. Chem. B Lett.
, vol.110
, pp. 15045-15048
-
-
Shi, Q.1
Izvekov, S.2
Voth, G.A.3
-
124
-
-
0001603545
-
DL POLY: Application to molecular simulation
-
Smith W., Yong C.W., Rodger P.M. DL POLY: Application to molecular simulation. Mol. Simul. 2002, 28:385-471.
-
(2002)
Mol. Simul.
, vol.28
, pp. 385-471
-
-
Smith, W.1
Yong, C.W.2
Rodger, P.M.3
-
125
-
-
61949390790
-
Systematic coarse-graining of a multicomponent lipid bilayer
-
Lu L., Voth G.A. Systematic coarse-graining of a multicomponent lipid bilayer. J. Phys. Chem. B 2009, 113:1501-1510.
-
(2009)
J. Phys. Chem. B
, vol.113
, pp. 1501-1510
-
-
Lu, L.1
Voth, G.A.2
-
126
-
-
77955487466
-
Multiscale coarse-graining of the protein energy landscape
-
Hills R.D., Lu L., Voth G.A. Multiscale coarse-graining of the protein energy landscape. PLoS Comput. Biol. 2010, 6:e10000827.
-
(2010)
PLoS Comput. Biol.
, vol.6
-
-
Hills, R.D.1
Lu, L.2
Voth, G.A.3
-
127
-
-
67651236198
-
The multiscale coarse-graining method. III. A test of pairwise additivity of the coarse-grained potential and of new basis functions for the variational calculation
-
Das A., Andersen H.C. The multiscale coarse-graining method. III. A test of pairwise additivity of the coarse-grained potential and of new basis functions for the variational calculation. J. Chem. Phys. 2009, 131:034102.
-
(2009)
J. Chem. Phys.
, vol.131
, pp. 034102
-
-
Das, A.1
Andersen, H.C.2
-
128
-
-
67650752138
-
The multiscale coarse-graining method. IV. Transferring coarse-grained potentials between temperatures
-
Krishna V., Noid W., Voth G.A. The multiscale coarse-graining method. IV. Transferring coarse-grained potentials between temperatures. J. Chem. Phys. 2009, 131:024103.
-
(2009)
J. Chem. Phys.
, vol.131
, pp. 024103
-
-
Krishna, V.1
Noid, W.2
Voth, G.A.3
-
129
-
-
77952397349
-
The multiscale coarse-graining method. V. Isothermal-isobaric ensemble
-
Das A., Andersen H.C. The multiscale coarse-graining method. V. Isothermal-isobaric ensemble. J. Chem. Phys. 2010, 132:164106.
-
(2010)
J. Chem. Phys.
, vol.132
, pp. 164106
-
-
Das, A.1
Andersen, H.C.2
-
130
-
-
77952398307
-
The multiscale coarse-graining method. VI. Implementation of three-body coarse-grained potentials
-
Larini L., Lu L., Voth G.A. The multiscale coarse-graining method. VI. Implementation of three-body coarse-grained potentials. J. Chem. Phys. 2010, 132:164107.
-
(2010)
J. Chem. Phys.
, vol.132
, pp. 164107
-
-
Larini, L.1
Lu, L.2
Voth, G.A.3
-
131
-
-
0037037945
-
Polymers near metal surfaces: Selective adsorption and global conformations
-
Site D.L., Abrams C.F., Kremer K. Polymers near metal surfaces: Selective adsorption and global conformations. Phys. Rev. Lett. 2002, 89:156103.
-
(2002)
Phys. Rev. Lett.
, vol.89
, pp. 156103
-
-
Site, D.L.1
Abrams, C.F.2
Kremer, K.3
-
132
-
-
1542316814
-
BPA-PC on a Ni(11) surface: The interplay between adsorption energy and conformational entropy for different chain-end modifications
-
Site D.L., Leon S., Kremer K. BPA-PC on a Ni(11) surface: The interplay between adsorption energy and conformational entropy for different chain-end modifications. J. Am. Chem. Soc. 2004, 126:2944.
-
(2004)
J. Am. Chem. Soc.
, vol.126
, pp. 2944
-
-
Site, D.L.1
Leon, S.2
Kremer, K.3
-
133
-
-
18744369718
-
Multiscale method for simulating protein-DNA complexes
-
Villa E., Balaeff A., Mahadevan L., Schulten K. Multiscale method for simulating protein-DNA complexes. Multiscale Model. Simul. 2004, 2:527.
-
(2004)
Multiscale Model. Simul.
, vol.2
, pp. 527
-
-
Villa, E.1
Balaeff, A.2
Mahadevan, L.3
Schulten, K.4
-
134
-
-
28844494903
-
Coarse-grained model of proteins incorporating atomistic detail of the active site
-
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.
-
(2005)
Phys. Rev. Lett.
, vol.95
, pp. 218102
-
-
Neri, M.1
Anselmi, C.2
Cascella, M.3
Maritan, A.4
Carloni, P.5
-
135
-
-
29144483372
-
Adaptive resolution molecular dynamics simulation: Changing the degrees of freedom on the fiy
-
Praprotnik M., Site D.L., Kremer K. Adaptive resolution molecular dynamics simulation: Changing the degrees of freedom on the fiy. J. Chem. Phys. 2005, 123:224106.
-
(2005)
J. Chem. Phys.
, vol.123
, pp. 224106
-
-
Praprotnik, M.1
Site, D.L.2
Kremer, K.3
-
136
-
-
35348848961
-
Energy conservation in adaptive hybrid atomistic/coarse-grained molecular dynamics
-
Ensing B., Nielsen S.O., Moore P.B., Klein M.L., Parrinello M. Energy conservation in adaptive hybrid atomistic/coarse-grained molecular dynamics. J. Chem. Theory Comput. 2007, 3:1100.
-
(2007)
J. Chem. Theory Comput.
, vol.3
, pp. 1100
-
-
Ensing, B.1
Nielsen, S.O.2
Moore, P.B.3
Klein, M.L.4
Parrinello, M.5
-
137
-
-
58049208953
-
Conservative algorithm for an adaptive change of resolution in mixed atomistic/coarse-grained multiscale simulations
-
Heyden A., Truhlar D.G. Conservative algorithm for an adaptive change of resolution in mixed atomistic/coarse-grained multiscale simulations. J. Chem. Theory Comput. 2008, 4:217.
-
(2008)
J. Chem. Theory Comput.
, vol.4
, pp. 217
-
-
Heyden, A.1
Truhlar, D.G.2
-
138
-
-
77957897253
-
Recent progress in adaptive multiscale molecular dynamics simulations of soft matter
-
Nielsen S.O., Bulo R.E., Moore P.B., Ensing B. Recent progress in adaptive multiscale molecular dynamics simulations of soft matter. Phys. Chem. Chem. Phys. 2010, 12:12401.
-
(2010)
Phys. Chem. Chem. Phys.
, vol.12
, pp. 12401
-
-
Nielsen, S.O.1
Bulo, R.E.2
Moore, P.B.3
Ensing, B.4
-
139
-
-
34547302112
-
Adaptive resolution simulation of liquid water
-
Praprotnik M. Adaptive resolution simulation of liquid water. J. Phys. Condens. Matter 2007, 16:292201.
-
(2007)
J. Phys. Condens. Matter
, vol.16
, pp. 292201
-
-
Praprotnik, M.1
-
140
-
-
38349025664
-
Modeling diffusive dynamics in adaptive resolution simulation of liquid water
-
Matysiak S., Clementi C., Praprotnik M., Kremer K., Site D.L. Modeling diffusive dynamics in adaptive resolution simulation of liquid water. J. Chem. Phys. 2008, 128:024503.
-
(2008)
J. Chem. Phys.
, vol.128
, pp. 024503
-
-
Matysiak, S.1
Clementi, C.2
Praprotnik, M.3
Kremer, K.4
Site, D.L.5
-
141
-
-
29244444027
-
Concurrent dual-resolution Monte Carlo simulation of liquid methane
-
Abrams C.F. Concurrent dual-resolution Monte Carlo simulation of liquid methane. J. Chem. Phys. 2005, 123:234101.
-
(2005)
J. Chem. Phys.
, vol.123
, pp. 234101
-
-
Abrams, C.F.1
-
142
-
-
73149092783
-
Solving the equations of motion for mixed atomistic and coarse-grained systems
-
Park J.H., Heyden A. Solving the equations of motion for mixed atomistic and coarse-grained systems. Mol. Simul. 2009, 35:962-973.
-
(2009)
Mol. Simul.
, vol.35
, pp. 962-973
-
-
Park, J.H.1
Heyden, A.2
-
143
-
-
33744807503
-
Adaptive resolution scheme for efficient hybrid atomistic-mesoscale molecular dynamics simulations of dense liquids
-
Praprotnik M., Site D.L., Kremer K. Adaptive resolution scheme for efficient hybrid atomistic-mesoscale molecular dynamics simulations of dense liquids. Phys. Rev. E 2006, 73:066701.
-
(2006)
Phys. Rev. E
, vol.73
, pp. 066701
-
-
Praprotnik, M.1
Site, D.L.2
Kremer, K.3
-
144
-
-
77952402284
-
Single-molecule dynamics of gating in a neurotransmitter transporter homologue
-
Zhao Y., Terry D., Shi L., Weinstein H., Blanchard S.C., Javitch J.A. Single-molecule dynamics of gating in a neurotransmitter transporter homologue. Nature 2010, 465:188-193.
-
(2010)
Nature
, vol.465
, pp. 188-193
-
-
Zhao, Y.1
Terry, D.2
Shi, L.3
Weinstein, H.4
Blanchard, S.C.5
Javitch, J.A.6
-
145
-
-
24644470065
-
Crystal structure of a bacterial homologue of Na(+) Cl(-)-dependent neurotransmitter transporters
-
Yamashita A., Singh S.K., Kawate T., Jin T., Gouaux E. Crystal structure of a bacterial homologue of Na(+) Cl(-)-dependent neurotransmitter transporters. Nature 2005, 437:215-223.
-
(2005)
Nature
, vol.437
, pp. 215-223
-
-
Yamashita, A.1
Singh, S.K.2
Kawate, T.3
Jin, T.4
Gouaux, E.5
-
146
-
-
0003464216
-
-
National Institute of Standards and Technology, Gaithersburg, MD
-
Linstrom P.J., Mallard W.G. NIST Chemistry WebBook, NIST Standard Reference Database Number 69 2011, National Institute of Standards and Technology, Gaithersburg, MD, p. 20899, http://webbook.nist.gov.
-
(2011)
NIST Chemistry WebBook, NIST Standard Reference Database Number 69
, pp. 20899
-
-
Linstrom, P.J.1
Mallard, W.G.2
-
147
-
-
60049083996
-
Comparative atomistic and coarse-grained study of water: What do we lose by coarse-graining?
-
Wang H., Junghaus C., Kremer K. Comparative atomistic and coarse-grained study of water: What do we lose by coarse-graining?. Eur. Phys. J. E 2009, 28:221-229.
-
(2009)
Eur. Phys. J. E
, vol.28
, pp. 221-229
-
-
Wang, H.1
Junghaus, C.2
Kremer, K.3
-
148
-
-
24144479792
-
Solvation free energies of amino acid side chain analogs for common molecular mechanics water models
-
Shirts M.R., Pande V.S. Solvation free energies of amino acid side chain analogs for common molecular mechanics water models. J. Chem. Phys. 2005, 122:134508.
-
(2005)
J. Chem. Phys.
, vol.122
, pp. 134508
-
-
Shirts, M.R.1
Pande, V.S.2
-
149
-
-
34247324361
-
Surface tension of the most popular models of water by using the test-area simulation method
-
Vega C., de Miguel E. Surface tension of the most popular models of water by using the test-area simulation method. J. Chem. Phys. 2007, 126:154707.
-
(2007)
J. Chem. Phys.
, vol.126
, pp. 154707
-
-
Vega, C.1
de Miguel, E.2
-
150
-
-
77950112700
-
A coarse-grained model based on morse potential for water and n-alkanes
-
Chiu S.-W., Scott H.L., Jakobsson E. A coarse-grained model based on morse potential for water and n-alkanes. J. Chem. Theory Comput. 2010, 6:851-863.
-
(2010)
J. Chem. Theory Comput.
, vol.6
, pp. 851-863
-
-
Chiu, S.-W.1
Scott, H.L.2
Jakobsson, E.3
-
151
-
-
79952076954
-
A simple, efficient polarizable coarse-grained water model for molecular dynamics simulations
-
Riniker S., van Gunsteren W.F. A simple, efficient polarizable coarse-grained water model for molecular dynamics simulations. J. Chem. Phys. 2011, 134:084110.
-
(2011)
J. Chem. Phys.
, vol.134
, pp. 084110
-
-
Riniker, S.1
van Gunsteren, W.F.2
-
152
-
-
77955561671
-
A new coarse-grained model for water: The importance of electrostatic interactions
-
Wu Z., Cui Q., Yethiraj A. A new coarse-grained model for water: The importance of electrostatic interactions. J. Phys. Chem. B 2010, 114:10524-10529.
-
(2010)
J. Phys. Chem. B
, vol.114
, pp. 10524-10529
-
-
Wu, Z.1
Cui, Q.2
Yethiraj, A.3
|