-
1
-
-
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
-
2
-
-
34247098754
-
Multiscale modeling of biomolecular systems: In serial and in parallel
-
Ayton, G. S.; Noid, W. G.; Voth, G. A. Multiscale modeling of biomolecular systems: in serial and in parallel Curr. Opin. Struct. Biol. 2007, 17, 192-198
-
(2007)
Curr. Opin. Struct. Biol.
, vol.17
, pp. 192-198
-
-
Ayton, G.S.1
Noid, W.G.2
Voth, G.A.3
-
3
-
-
63449129633
-
Insights from coarse-grained Go models for protein folding and dynamics
-
Hills, R. D., Jr.; Brooks, C. L., III Insights from coarse-grained Go models for protein folding and dynamics Int. J. Mol. Sci. 2009, 10, 889-905
-
(2009)
Int. J. Mol. Sci.
, vol.10
, pp. 889-905
-
-
Hills, Jr.R.D.1
Brooks III, C.L.2
-
4
-
-
84861773417
-
Coarse-grained molecular simulations of large biomolecules
-
Takada, S. Coarse-grained molecular simulations of large biomolecules Curr. Opin. Struct. Biol. 2012, 22, 130-137
-
(2012)
Curr. Opin. Struct. Biol.
, vol.22
, pp. 130-137
-
-
Takada, S.1
-
5
-
-
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. 2006, 157, 579-592
-
(2006)
J. Struct. Biol.
, vol.157
, pp. 579-592
-
-
Shih, A.Y.1
Freddolino, P.L.2
Arkhipov, A.3
Schulten, K.4
-
6
-
-
5244275439
-
Stochastic dynamics simulations of macromolecular diffusion in a model of the cytoplasm of Escherichia coli
-
Bicout, D. J.; Field, M. J. Stochastic dynamics simulations of macromolecular diffusion in a model of the cytoplasm of Escherichia coli J. Phys. Chem. 1996, 100, 2489-2497
-
(1996)
J. Phys. Chem.
, vol.100
, pp. 2489-2497
-
-
Bicout, D.J.1
Field, M.J.2
-
7
-
-
43849103490
-
Coarse-grained molecular simulation of diffusion and reaction kinetics in a crowded virtual cytoplasm
-
Ridgway, D.; Broderick, G.; Lopez-Campistrous, A.; Ru'aini, M.; Winter, P.; Hamilton, M.; Boulanger, P.; Kovalenko, A.; Ellison, M. J. Coarse-grained molecular simulation of diffusion and reaction kinetics in a crowded virtual cytoplasm Biophys. J. 2008, 94, 3748-3759
-
(2008)
Biophys. J.
, vol.94
, pp. 3748-3759
-
-
Ridgway, D.1
Broderick, G.2
Lopez-Campistrous, A.3
Ru'Aini, M.4
Winter, P.5
Hamilton, M.6
Boulanger, P.7
Kovalenko, A.8
Ellison, M.J.9
-
8
-
-
77950792003
-
Diffusion, crowding, and protein stability in a dynamic molecular model of the bacterial cytoplasm
-
McGuffee, S. R.; Elcock, A. H. Diffusion, crowding, and protein stability in a dynamic molecular model of the bacterial cytoplasm PLoS Comput. Biol. 2010, 6, e1000694
-
(2010)
PLoS Comput. Biol.
, vol.6
, pp. 1000694
-
-
McGuffee, S.R.1
Elcock, A.H.2
-
9
-
-
78649876151
-
Crowding and hydrodynamic interactions likely dominate in vivo macromolecular motion
-
Ando, T.; Skolnick, J. Crowding and hydrodynamic interactions likely dominate in vivo macromolecular motion Proc. Natl. Acad. Sci. U.S.A. 2010, 107, 18457-18462
-
(2010)
Proc. Natl. Acad. Sci. U.S.A.
, vol.107
, pp. 18457-18462
-
-
Ando, T.1
Skolnick, J.2
-
10
-
-
0031768735
-
Protein interactions in solution characterized by light and neutron scattering: Comparison of lysozyme and chymotrypsinogen
-
Velev, O. D.; Kaler, E. W.; Lenhoff, A. M. Protein interactions in solution characterized by light and neutron scattering: Comparison of lysozyme and chymotrypsinogen Biophys. J. 1998, 75, 2682-2697
-
(1998)
Biophys. J.
, vol.75
, pp. 2682-2697
-
-
Velev, O.D.1
Kaler, E.W.2
Lenhoff, A.M.3
-
11
-
-
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
-
12
-
-
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. Theor. Comput. 2008, 4, 819-834
-
(2008)
J. Chem. Theor. 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
-
13
-
-
73949130043
-
MARTINI coarse-grained force field: Extension to carbohydrates
-
Lopez, C. A.; Rzepiela, A. J.; de Vries, A. H.; Dijkhuizen, L.; Hünenberger, P. H.; Marrink, S. J. MARTINI coarse-grained force field: Extension to carbohydrates J. Chem. Theor. Comput. 2009, 5, 3195-3210
-
(2009)
J. Chem. Theor. Comput.
, vol.5
, pp. 3195-3210
-
-
Lopez, C.A.1
Rzepiela, A.J.2
De Vries, A.H.3
Dijkhuizen, L.4
Hünenberger, P.H.5
Marrink, S.J.6
-
14
-
-
46249092554
-
GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation
-
Hess, B.; Kutzner, C.; van der Spoel, D.; Lindahl, E. GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation J. Chem. Theor. Comput. 2008, 4, 435-447
-
(2008)
J. Chem. Theor. Comput.
, vol.4
, pp. 435-447
-
-
Hess, B.1
Kutzner, C.2
Van Der Spoel, D.3
Lindahl, E.4
-
15
-
-
33748804712
-
Atomically detailed simulations of concentrated protein solutions: The effects of salt, pH, point mutations, and protein concentration in simulations of 1000-molecule systems
-
McGuffee, S. R.; Elcock, A. H. Atomically detailed simulations of concentrated protein solutions: The effects of salt, pH, point mutations, and protein concentration in simulations of 1000-molecule systems J. Am. Chem. Soc. 2006, 128, 12098-12110
-
(2006)
J. Am. Chem. Soc.
, vol.128
, pp. 12098-12110
-
-
McGuffee, S.R.1
Elcock, A.H.2
-
16
-
-
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. Theor. Comput. 2009, 5, 2531-2543
-
(2009)
J. Chem. Theor. Comput.
, vol.5
, pp. 2531-2543
-
-
Periole, X.1
Cavalli, M.2
Marrink, S.J.3
Ceruso, M.A.4
-
17
-
-
77955503561
-
Polarizable water model for the coarse-grained MARTINI force field
-
Yesylevskyy, S. O.; Schäfer, L. V.; Sengupta, D.; Marrink, S. J. Polarizable water model for the coarse-grained MARTINI force field PLoS Comput. Biol. 2010, 6, e1000810
-
(2010)
PLoS Comput. Biol.
, vol.6
, pp. 1000810
-
-
Yesylevskyy, S.O.1
Schäfer, L.V.2
Sengupta, D.3
Marrink, S.J.4
-
18
-
-
84863535732
-
Structural determinants of the supra-molecular organization of G protein-coupled receptors in bilayers
-
Periole, X.; Knepp, A. M.; Sakmar, T. P.; Marrink, S. J.; Huber, T. Structural determinants of the supra-molecular organization of G protein-coupled receptors in bilayers J. Am. Chem. Soc. 2012, 134, 10959-10965
-
(2012)
J. Am. Chem. Soc.
, vol.134
, pp. 10959-10965
-
-
Periole, X.1
Knepp, A.M.2
Sakmar, T.P.3
Marrink, S.J.4
Huber, T.5
-
19
-
-
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
-
20
-
-
0034294024
-
Multidimensional replica-exchange method for free-energy calculations
-
Sugita, Y.; Kitao, A.; Okamoto, Y. Multidimensional replica-exchange method for free-energy calculations J. Chem. Phys. 2000, 113, 6042-6051
-
(2000)
J. Chem. Phys.
, vol.113
, pp. 6042-6051
-
-
Sugita, Y.1
Kitao, A.2
Okamoto, Y.3
-
21
-
-
84986519238
-
The weighted histogram analysis method for free-energy calculations on biomolecules. I. The method
-
Kumar, S.; Bouzida, D.; Swendsen, R. H.; Kollman, P. A.; Rosenberg, J. M. The weighted histogram analysis method for free-energy calculations on biomolecules. I. The method J. Comput. Chem. 1992, 13, 1011-1021
-
(1992)
J. Comput. Chem.
, vol.13
, pp. 1011-1021
-
-
Kumar, S.1
Bouzida, D.2
Swendsen, R.H.3
Kollman, P.A.4
Rosenberg, J.M.5
-
23
-
-
0031723926
-
Molecular origins of osmotic second virial coefficients of proteins
-
Neal, B. L.; Asthagiri, D.; Lenhoff, A. M. Molecular origins of osmotic second virial coefficients of proteins Biophys. J. 1998, 75, 2469-2477
-
(1998)
Biophys. J.
, vol.75
, pp. 2469-2477
-
-
Neal, B.L.1
Asthagiri, D.2
Lenhoff, A.M.3
-
24
-
-
84864225957
-
Atomic detail Brownian dynamics simulations of concentrated protein solutions with a mean field treatment of hydrodynamic interactions
-
Mereghetti, P.; Wade, R. C. Atomic detail Brownian dynamics simulations of concentrated protein solutions with a mean field treatment of hydrodynamic interactions J. Phys. Chem. B 2012, 116, 8523-8533
-
(2012)
J. Phys. Chem. B
, vol.116
, pp. 8523-8533
-
-
Mereghetti, P.1
Wade, R.C.2
-
25
-
-
0034308128
-
Measured and calculated effects of mutations in bacteriophage T4 lysozyme on interactions in solution
-
Chang, R. C.; Asthagiri, D.; Lenhoff, A. M. Measured and calculated effects of mutations in bacteriophage T4 lysozyme on interactions in solution Proteins-Struct. Funct. Genet. 2000, 41, 123-13
-
(2000)
Proteins - Struct. Funct. Genet.
, vol.41
, pp. 123-213
-
-
Chang, R.C.1
Asthagiri, D.2
Lenhoff, A.M.3
-
26
-
-
1942473133
-
Direct measurement of protein osmotic second virial cross coefficients by cross-interaction chromatography
-
Tessier, P. M.; Sandler, S. I.; Lenhoff, A. M. Direct measurement of protein osmotic second virial cross coefficients by cross-interaction chromatography Protein Sci. 2004, 13, 1379-1390
-
(2004)
Protein Sci.
, vol.13
, pp. 1379-1390
-
-
Tessier, P.M.1
Sandler, S.I.2
Lenhoff, A.M.3
-
27
-
-
2342648129
-
Chromatographic measurement of interactions between unlike proteins
-
Teske, C. A.; Blanch, H. W.; Prausnitz, J. M. Chromatographic measurement of interactions between unlike proteins Fluid Phase Equilib. 2004, 219, 139-148
-
(2004)
Fluid Phase Equilib.
, vol.219
, pp. 139-148
-
-
Teske, C.A.1
Blanch, H.W.2
Prausnitz, J.M.3
-
28
-
-
0029289456
-
Excluded volume contribution to the osmotic second virial coefficient for proteins
-
Neal, B. L.; Lenhoff, A. M. Excluded volume contribution to the osmotic second virial coefficient for proteins AIChE J. 1995, 41, 1010-1014
-
(1995)
AIChE J.
, vol.41
, pp. 1010-1014
-
-
Neal, B.L.1
Lenhoff, A.M.2
-
29
-
-
0035142983
-
Calculation of weak protein-protein interactions: The pH dependence of the second virial coefficient
-
Elcock, A. H.; McCammon, J. A. Calculation of weak protein-protein interactions: The pH dependence of the second virial coefficient Biophys. J. 2001, 80, 613-625
-
(2001)
Biophys. J.
, vol.80
, pp. 613-625
-
-
Elcock, A.H.1
McCammon, J.A.2
-
30
-
-
0242290876
-
A mesoscopic model for protein-protein interactions in solution
-
Lund, M.; Jönsson, B. A mesoscopic model for protein-protein interactions in solution Biophys. J. 2003, 85, 2940-2947
-
(2003)
Biophys. J.
, vol.85
, pp. 2940-2947
-
-
Lund, M.1
Jönsson, B.2
-
31
-
-
17144365075
-
On the charge regulation of proteins
-
Lund, M.; Jönsson, B. On the charge regulation of proteins Biochemistry 2005, 44, 5722-5727
-
(2005)
Biochemistry
, vol.44
, pp. 5722-5727
-
-
Lund, M.1
Jönsson, B.2
-
32
-
-
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
-
33
-
-
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
-
34
-
-
78649859456
-
Brownian dynamics simulation of protein solutions: Structural and dynamic properties
-
Mereghetti, P.; Gabdoulline, R. R.; Wade, R. C. Brownian dynamics simulation of protein solutions: Structural and dynamic properties Biophys. J. 2010, 99, 3782-3791
-
(2010)
Biophys. J.
, vol.99
, pp. 3782-3791
-
-
Mereghetti, P.1
Gabdoulline, R.R.2
Wade, R.C.3
-
35
-
-
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
-
36
-
-
79952153989
-
Lipid packing drives the segregation of transmembrane helices into disordered lipid domains in model biomembranes
-
Schafer, L. V.; de Jong, D. H.; Holt, A.; Rzepiela, A. J.; de Vries, A. H.; Poolman, B.; Killian, J. A.; Marrink, S. J. Lipid packing drives the segregation of transmembrane helices into disordered lipid domains in model biomembranes Proc. Natl. Acad. Sci. U.S.A. 2011, 108, 1343-1348
-
(2011)
Proc. Natl. Acad. Sci. U.S.A.
, vol.108
, pp. 1343-1348
-
-
Schafer, L.V.1
De Jong, D.H.2
Holt, A.3
Rzepiela, A.J.4
De Vries, A.H.5
Poolman, B.6
Killian, J.A.7
Marrink, S.J.8
-
37
-
-
84858300656
-
Dimerization of amino acid side chains: Lessons from the comparison of different forcefields
-
de Jong, D. H.; Periole, X.; Marrink, S. J. Dimerization of amino acid side chains: Lessons from the comparison of different forcefields J. Chem. Theor. Comput. 2011, 8, 1003-1014
-
(2011)
J. Chem. Theor. Comput.
, vol.8
, pp. 1003-1014
-
-
De Jong, D.H.1
Periole, X.2
Marrink, S.J.3
-
38
-
-
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.; Pomes, S.; 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. Theor. Comput. 2012, 8, 1774-1785
-
(2012)
J. Chem. Theor. Comput.
, vol.8
, pp. 1774-1785
-
-
Seo, M.1
Rauscher, S.2
Pomes, S.3
Tieleman, D.P.4
-
39
-
-
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. Theor. Comput. 2012, 9, 687-697
-
(2012)
J. Chem. Theor. 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
-
40
-
-
84884197976
-
Constant pH simulations with the coarse-grained MARTINI model: Application to oleic acid aggregates
-
10.1139/cjc-2013-0010
-
Bennett, W.; Chen, A.; Donnini, S.; Groenhof, G.; Tieleman, P. Constant pH simulations with the coarse-grained MARTINI model: Application to oleic acid aggregates Can. J. Chem. 2013, 10.1139/cjc-2013-0010
-
(2013)
Can. J. Chem.
-
-
Bennett, W.1
Chen, A.2
Donnini, S.3
Groenhof, G.4
Tieleman, P.5
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