-
4
-
-
4644236471
-
Hydrophobic collapse in multidomain protein folding
-
R. Zhou, X. Huang, C.J. Margulius, B.J. Berne. Hydrophobic collapse in multidomain protein folding. Science, 305, 1605 (2004).
-
(2004)
Science
, vol.305
, pp. 1605
-
-
Zhou, R.1
Huang, X.2
Margulius, C.J.3
Berne, B.J.4
-
5
-
-
24344448662
-
Observation of a dewetting transition in the melittin tetramer collapse
-
P. Liu, X. Huang, R. Zhou, B.J. Berne. Observation of a dewetting transition in the melittin tetramer collapse. Nature, 437, 159 (2005).
-
(2005)
Nature
, vol.437
, pp. 159
-
-
Liu, P.1
Huang, X.2
Zhou, R.3
Berne, B.J.4
-
6
-
-
0034662849
-
New perspectives on hydrophobic effects
-
G. Hummer, S. Garde, A.E. Garcia, L.R. Pratt. New perspectives on hydrophobic effects. Chem. Phys., 258, 349 (2000).
-
(2000)
Chem. Phys.
, vol.258
, pp. 349
-
-
Hummer, G.1
Garde, S.2
Garcia, A.E.3
Pratt, L.R.4
-
7
-
-
0034300332
-
Dynamics of capillary evaporation, i. Effect of morphology of hydrophobic surfaces
-
A. Luzar, K. Leung. Dynamics of capillary evaporation, i. Effect of morphology of hydrophobic surfaces. J. Chem. Phys., 113, 5836 (2000).
-
(2000)
J. Chem. Phys.
, vol.113
, pp. 5836
-
-
Luzar, A.1
Leung, K.2
-
8
-
-
0037435840
-
Dynamics of capillary drying in water
-
K. Leung, A. Luzar, D. Bratko. Dynamics of capillary drying in water. Phys. Rev. Lett., 90(1-4), 65502 (2003).
-
(2003)
Phys. Rev. Lett.
, vol.90
, Issue.1-4
, pp. 65502
-
-
Leung, K.1
Luzar, A.2
Bratko, D.3
-
9
-
-
0037089017
-
The sgb/np hydration free energy model baed on the surface generalized born solvent reaction field and novel non-polar hydration free energy estimators
-
E. Gallicchio, L.Y. Zhang, R.M. Levy. The sgb/np hydration free energy model baed on the surface generalized born solvent reaction field and novel non-polar hydration free energy estimators. J. Comput. Chem., 23, 517 (2002).
-
(2002)
J. Comput. Chem.
, vol.23
, pp. 517
-
-
Gallicchio, E.1
Zhang, L.Y.2
Levy, R.M.3
-
10
-
-
3042801661
-
Free energy surfaces of betahairpin and alpha-helical peptides generated by replica exchange molecular dynamics with the agbnp implicit solvent model
-
E. Gallicchio, L.Y. Zhang, R.M. Levy. Free energy surfaces of betahairpin and alpha-helical peptides generated by replica exchange molecular dynamics with the agbnp implicit solvent model. Proteins, 56, 310 (2004).
-
(2004)
Proteins
, vol.56
, pp. 310
-
-
Gallicchio, E.1
Zhang, L.Y.2
Levy, R.M.3
-
11
-
-
0033654297
-
Generalized born models of macromolecular solvation effects
-
D. Bashford, D. Case. Generalized born models of macromolecular solvation effects. Annu. Rev. Phys. Chem., 51, 129 (2000).
-
(2000)
Annu. Rev. Phys. Chem.
, vol.51
, pp. 129
-
-
Bashford, D.1
Case, D.2
-
12
-
-
20644449471
-
A modification of the generalized born model suitable for macromolecules
-
A. Onufriev, D. Bashford, D. Case. A modification of the generalized born model suitable for macromolecules. J. Phys. Chem. B, 104, 3712 (2000).
-
(2000)
J. Phys. Chem. B
, vol.104
, pp. 3712
-
-
Onufriev, A.1
Bashford, D.2
Case, D.3
-
13
-
-
0002775934
-
Interaction models for water in relation to protein hydration
-
Pullman (Ed.), Dordrecht, Reidel
-
H.J.C. Berendsen, J.P.M. Postma, W.F. van Gunsteren, J. Hermans. Interaction models for water in relation to protein hydration. In Intermolecular Forces, B. Pullman (Ed.), pp. 331-342, Dordrecht, Reidel (1981).
-
(1981)
Intermolecular Forces, B
, pp. 331-342
-
-
Berendsen, H.J.C.1
Postma, J.P.M.2
Van Gunsteren, W.F.3
Hermans, J.4
-
14
-
-
0029016182
-
Classical electrostatics in biology and chemistry
-
B. Honig, A. Nicholls. Classical electrostatics in biology and chemistry. Science, 268, 1144 (1995).
-
(1995)
Science
, vol.268
, pp. 1144
-
-
Honig, B.1
Nicholls, A.2
-
15
-
-
0344778061
-
Semianalytical treatment of solvation for molecular mechanics and dynamics
-
W.C. Still, A. Tempczyk, R.C. Hawley, T. Hendrickson. Semianalytical treatment of solvation for molecular mechanics and dynamics. J. Am. Chem. Soc., 112, 6127 (1990).
-
(1990)
J. Am. Chem. Soc.
, vol.112
, pp. 6127
-
-
Still, W.C.1
Tempczyk, A.2
Hawley, R.C.3
Hendrickson, T.4
-
16
-
-
0035909921
-
The free energy landscape for β-hairpin folding in explicit water
-
R. Zhou, B.J. Berne, R. Germain. The free energy landscape for β-hairpin folding in explicit water. Proc. Natl. Acad. Sci. USA, 98, 14931 (2001).
-
(2001)
Proc. Natl. Acad. Sci. USA
, vol.98
, pp. 14931
-
-
Zhou, R.1
Berne, B.J.2
Germain, R.3
-
17
-
-
0036789950
-
Can a continuum solvent model reproduce the free energy landscape of a β-hairpin folding in water?
-
R. Zhou, B.J. Berne. Can a continuum solvent model reproduce the free energy landscape of a β-hairpin folding in water? Proc. Natl. Acad. Sci. USA, 99, 12777 (2002).
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 12777
-
-
Zhou, R.1
Berne, B.J.2
-
18
-
-
0141704162
-
Free energy landscape of protein folding in water: Explicit vs. implicit solvent
-
R. Zhou. Free energy landscape of protein folding in water: explicit vs. implicit solvent. Proteins, 53, 148 (2003).
-
(2003)
Proteins
, vol.53
, pp. 148
-
-
Zhou, R.1
-
19
-
-
2942700087
-
Comment on "can a continuum solvent model reproduce the free energy landscape of a beta-hairpin folding in water?"
-
R. Zhou, G. Krilov, B.J. Berne. Comment on "can a continuum solvent model reproduce the free energy landscape of a beta-hairpin folding in water?". J. Phys. Chem. B., 108, 7528 (2004).
-
(2004)
J. Phys. Chem. B
, vol.108
, pp. 7528
-
-
Zhou, R.1
Krilov, G.2
Berne, B.J.3
-
20
-
-
33749605193
-
Is poisson-boltzmann theory insufficient for protein folding simulations?
-
T.Z. Lwin, R. Zhou, R. Luo. Is poisson-boltzmann theory insufficient for protein folding simulations? J. Chem. Phys., 124, 34902 (2006).
-
(2006)
J. Chem. Phys.
, vol.124
, pp. 34902
-
-
Lwin, T.Z.1
Zhou, R.2
Luo, R.3
-
21
-
-
33745960026
-
Investigation of salt bridge stability in a generalized born solvent model
-
R. Geney, M. Layten, R. Gomperts, V. Hornak, C. Simmerling. Investigation of salt bridge stability in a generalized born solvent model. J. Chem. Theory Comput., 2, 115 (2006).
-
(2006)
J. Chem. Theory Comput.
, vol.2
, pp. 115
-
-
Geney, R.1
Layten, M.2
Gomperts, R.3
Hornak, V.4
Simmerling, C.5
-
22
-
-
0029912748
-
Development and testing of the opls all-atom froce field on conformational energetics and properties of organic liquids
-
W.L. Jorgensen, D. Maxwell, J. Tirado-Rives. Development and testing of the opls all-atom froce field on conformational energetics and properties of organic liquids. J. Am. Chem. Soc., 118, 11225 (1996).
-
(1996)
J. Am. Chem. Soc.
, vol.118
, pp. 11225
-
-
Jorgensen, W.L.1
Maxwell, D.2
Tirado-Rives, J.3
-
23
-
-
0031167555
-
Atomic radii for continuum electrostatics calculations based on molecular dynamics free energy simulations
-
M. Nina, D. Belglov, B. Boux. Atomic radii for continuum electrostatics calculations based on molecular dynamics free energy simulations. J. Phys. Chem. B. 101, 5239 (1997).
-
(1997)
J. Phys. Chem. B
, vol.101
, pp. 5239
-
-
Nina, M.1
Belglov, D.2
Boux, B.3
-
24
-
-
23844475490
-
Optimized radii for Poisson-Boltzmann calculations with the amber force field
-
J.M. Swanson, S.A. Adcock, J.A. McCammon. Optimized radii for Poisson-Boltzmann calculations with the amber force field. J. Chem. Theory Comput., 1, 484 (2005).
-
(2005)
J. Chem. Theory Comput.
, vol.1
, pp. 484
-
-
Swanson, J.M.1
Adcock, S.A.2
McCammon, J.A.3
-
25
-
-
0001246294
-
Generalized born model based on a surface integral formulation
-
A. Ghosh, C.S. Rapp, R.A. Friesner. Generalized born model based on a surface integral formulation. J. Phys. Chem. B, 102, 10983 (1998).
-
(1998)
J. Phys. Chem. B
, vol.102
, pp. 10983
-
-
Ghosh, A.1
Rapp, C.S.2
Friesner, R.A.3
-
26
-
-
0037120697
-
Combination between global and local methods for solving an optimization problem over the efficient set
-
H.A. Thi, D.T. Pham, N.V. Thoai. Combination between global and local methods for solving an optimization problem over the efficient set. Eur. J. Oper. Res., 142, 258 (2002).
-
(2002)
Eur. J. Oper. Res.
, vol.142
, pp. 258
-
-
Thi, H.A.1
Pham, D.T.2
Thoai, N.V.3
-
27
-
-
0000538815
-
Analytical molecular surface calculation
-
M.L. Connolly. Analytical molecular surface calculation. J. Appl. Cryst., 16, 548 (1983).
-
(1983)
J. Appl. Cryst.
, vol.16
, pp. 548
-
-
Connolly, M.L.1
-
28
-
-
0038502170
-
Folding dynamics and mechanism of β-hairpin formation
-
V. Munoz, P.A. Thompson, J. Hofrichter, W.A. Eaton. Folding dynamics and mechanism of β-hairpin formation. Nature, 390, 196 (1997).
-
(1997)
Nature
, vol.390
, pp. 196
-
-
Munoz, V.1
Thompson, P.A.2
Hofrichter, J.3
Eaton, W.A.4
-
29
-
-
0032568537
-
A statistical mechanical model for β-hairpin kinetics
-
V. Munoz, E.R. Henry, J. Hofrichter, W.A. Eaton. A statistical mechanical model for β-hairpin kinetics. Proc. Natl., Acad, Sci. USA, 95, 5872 (1998).
-
(1998)
Proc. Natl., Acad, Sci. USA
, vol.95
, pp. 5872
-
-
Munoz, V.1
Henry, E.R.2
Hofrichter, J.3
Eaton, W.A.4
-
30
-
-
0029070488
-
Folding of protein g b1 domain studied by the conformational characterization of fragments comprising its secondary structure elements
-
F.J. Blanco, L. Serrano. Folding of protein g b1 domain studied by the conformational characterization of fragments comprising its secondary structure elements. Eur. J. Biochem., 230, 634 (1995).
-
(1995)
Eur. J. Biochem.
, vol.230
, pp. 634
-
-
Blanco, F.J.1
Serrano, L.2
-
31
-
-
0035850758
-
β-Hairpin folding simulation in atomistic detail
-
B. Zagrovic, E.J. Sorin, V.S. Pande. β-Hairpin folding simulation in atomistic detail. J. Mol. Biol., 313, 151 (2001).
-
(2001)
J. Mol. Biol.
, vol.313
, pp. 151
-
-
Zagrovic, B.1
Sorin, E.J.2
Pande, V.S.3
-
32
-
-
0001616080
-
Replica-exchange molecular dynamics method for protein folding
-
Y. Sugita, Y. Okamoto. Replica-exchange molecular dynamics method for protein folding. Chem. Phys. Lett., 314, 141 (1999).
-
(1999)
Chem. Phys. Lett.
, vol.314
, pp. 141
-
-
Sugita, Y.1
Okamoto, Y.2
-
33
-
-
0344824394
-
Tip-cage: Folding free energy landscape in explicit water
-
R. Zhou, Tip-cage: folding free energy landscape in explicit water. Proc. Natl. Acad. Sci. USA, 100, 13280 (2003).
-
(2003)
Proc. Natl. Acad. Sci. USA
, vol.100
, pp. 13280
-
-
Zhou, R.1
-
34
-
-
0035312551
-
Macromolecular electrostatics; continuum models and their growing pains
-
T. Simonson. Macromolecular electrostatics; continuum models and their growing pains. Curr. Opin. Struct. Biol., 11, 243 (2001).
-
(2001)
Curr. Opin. Struct. Biol.
, vol.11
, pp. 243
-
-
Simonson, T.1
-
35
-
-
0035451052
-
What are the dielectric 'constants' of proteins and how to validate electrostatic models
-
C.N. Schutz, A. Warshel. What are the dielectric 'constants' of proteins and how to validate electrostatic models. Proteins, 44, 400 (2001).
-
(2001)
Proteins
, vol.44
, pp. 400
-
-
Schutz, C.N.1
Warshel, A.2
-
36
-
-
0040321024
-
Experimental measurement of the effective dielectric in the hydrophobic core of a protein
-
E. Garcia-Moreno, J. Dwyer, A. Gittis, E. Lattman, D. Spenser, W. Stites. Experimental measurement of the effective dielectric in the hydrophobic core of a protein. Biophys. Chem., 64, 211 (1997).
-
(1997)
Biophys. Chem.
, vol.64
, pp. 211
-
-
Garcia-Moreno, E.1
Dwyer, J.2
Gittis, A.3
Lattman, E.4
Spenser, D.5
Stites, W.6
|