-
1
-
-
51849180822
-
The Role of Solvent Models in Stabilizing Nonclassical Ions
-
Babu, C. S.; Tembe, B. L. The Role of Solvent Models in Stabilizing Nonclassical Ions J. Chem. Sci. 1987, 98, 235-240
-
(1987)
J. Chem. Sci.
, vol.98
, pp. 235-240
-
-
Babu, C.S.1
Tembe, B.L.2
-
2
-
-
34447297323
-
Energetics of Protein Folding
-
Baldwin, R. Energetics of Protein Folding J. Mol. Biol. 2007, 371, 283-301
-
(2007)
J. Mol. Biol.
, vol.371
, pp. 283-301
-
-
Baldwin, R.1
-
3
-
-
84961981091
-
Implicit Solvation Models: Equilibria, Structure, Spectra, and Dynamics
-
Cramer, C. J.; Truhlar, D. G. Implicit Solvation Models: Equilibria, Structure, Spectra, and Dynamics Chem. Rev. 1999, 99, 2161-2200
-
(1999)
Chem. Rev.
, vol.99
, pp. 2161-2200
-
-
Cramer, C.J.1
Truhlar, D.G.2
-
4
-
-
38949141177
-
Continuum Molecular Electrostatics, Salt effects, and Counterion Binding-A Review of the Poisson-Boltzmann Theory and its Modifications
-
Grochowski, P.; Trylska, J. Continuum Molecular Electrostatics, Salt effects, and Counterion Binding-A Review of the Poisson-Boltzmann Theory and its Modifications Biopolymers 2008, 89, 93-113
-
(2008)
Biopolymers
, vol.89
, pp. 93-113
-
-
Grochowski, P.1
Trylska, J.2
-
5
-
-
0033654297
-
Generalized Born Models of Macromolecular Solvation Effects
-
Bashford, D.; Case, D. A. Generalized Born Models of Macromolecular Solvation Effects Annu. Rev. Phys. Chem. 2000, 51, 129-152
-
(2000)
Annu. Rev. Phys. Chem.
, vol.51
, pp. 129-152
-
-
Bashford, D.1
Case, D.A.2
-
6
-
-
0028218493
-
A Global Model of the Protein-Solvent Interface
-
Lounnas, V.; Pettitt, B. M.; Phillips, G. N., Jr. A Global Model of the Protein-Solvent Interface Biophys. J. 1994, 66, 601-614
-
(1994)
Biophys. J.
, vol.66
, pp. 601-614
-
-
Lounnas, V.1
Pettitt, B.M.2
Phillips Jr., G.N.3
-
7
-
-
0036286851
-
Solvation and Hydration of Proteins and Nucleic Acids: A Theoretical View of Simulation and Experiment
-
Makarov, V.; Pettitt, B. M.; Feig, M. Solvation and Hydration of Proteins and Nucleic Acids: A Theoretical View of Simulation and Experiment Acc. Chem. Res. 2002, 35, 376-384
-
(2002)
Acc. Chem. Res.
, vol.35
, pp. 376-384
-
-
Makarov, V.1
Pettitt, B.M.2
Feig, M.3
-
8
-
-
79952001306
-
Electrostatic Solvation Free Energy of Amino Acid Side Chain Analogs: Implications for the Validity of Electrostatic Linear Response in Water
-
Lin, B.; Pettitt, B. M. Electrostatic Solvation Free Energy of Amino Acid Side Chain Analogs: Implications for the Validity of Electrostatic Linear Response in Water J. Comput. Chem. 2011, 32, 878-885
-
(2011)
J. Comput. Chem.
, vol.32
, pp. 878-885
-
-
Lin, B.1
Pettitt, B.M.2
-
9
-
-
0032233055
-
Computer Simulations with Explicit Solvent: Recent Progress in the Thermodynamic Decomposition of Free Energies and in Modeling Electrostatic Effects
-
Levy, R. M.; Gallicchio, E. Computer Simulations with Explicit Solvent: Recent Progress in the Thermodynamic Decomposition of Free Energies and in Modeling Electrostatic Effects Annu. Rev. Phys. Chem. 1998, 49, 531-567
-
(1998)
Annu. Rev. Phys. Chem.
, vol.49
, pp. 531-567
-
-
Levy, R.M.1
Gallicchio, E.2
-
10
-
-
34250928962
-
Volumes and Heats of Hydration of Ions
-
Born, M. Volumes and Heats of Hydration of Ions Z. Phys. 1920, 1, 45-48
-
(1920)
Z. Phys.
, vol.1
, pp. 45-48
-
-
Born, M.1
-
11
-
-
0009515513
-
The Electrostatic Free Energy of Globular Protein Ions in Aqueous Salt Solution
-
Tanford, C. The Electrostatic Free Energy of Globular Protein Ions in Aqueous Salt Solution J. Phys. Chem. 1955, 59, 788-793
-
(1955)
J. Phys. Chem.
, vol.59
, pp. 788-793
-
-
Tanford, C.1
-
12
-
-
0021813940
-
On the Calculation of Electrostatic Interactions in Proteins
-
Gilson, M. K.; Rashin, A.; Fine, R.; Honig, B. On the Calculation of Electrostatic Interactions in Proteins J. Mol. Biol. 1985, 184, 503-516
-
(1985)
J. Mol. Biol.
, vol.184
, pp. 503-516
-
-
Gilson, M.K.1
Rashin, A.2
Fine, R.3
Honig, B.4
-
13
-
-
0022070055
-
The Physical Origin of the Low Solubility of Nonpolar Solutes in Water
-
Lee, B. The Physical Origin of the Low Solubility of Nonpolar Solutes in Water Biopolymers 1985, 24, 813-823
-
(1985)
Biopolymers
, vol.24
, pp. 813-823
-
-
Lee, B.1
-
14
-
-
0032867608
-
A "universal" Surface Area Correlation for Molecular Hydrophobic Phenomena
-
Ashbaugh, H. S.; Kaler, E. W.; Paulaitis, M. E. A "Universal" Surface Area Correlation for Molecular Hydrophobic Phenomena J. Am. Chem. Soc. 1999, 121, 9243-9244
-
(1999)
J. Am. Chem. Soc.
, vol.121
, pp. 9243-9244
-
-
Ashbaugh, H.S.1
Kaler, E.W.2
Paulaitis, M.E.3
-
15
-
-
0011960339
-
Hydrophobicity at Small and Large Length Scales
-
Lum, K.; Chandler, D.; Weeks, J. D. Hydrophobicity at Small and Large Length Scales J. Phys. Chem. B 1999, 103, 4570-4577
-
(1999)
J. Phys. Chem. B
, vol.103
, pp. 4570-4577
-
-
Lum, K.1
Chandler, D.2
Weeks, J.D.3
-
16
-
-
0037187108
-
The Hydrophobic Effect and the Influence of Solute-Solvent Attractions
-
Huang, D. M.; Chandler, D. The Hydrophobic Effect and the Influence of Solute-Solvent Attractions J. Phys. Chem. B 2002, 106, 2047-2053
-
(2002)
J. Phys. Chem. B
, vol.106
, pp. 2047-2053
-
-
Huang, D.M.1
Chandler, D.2
-
17
-
-
0036423588
-
Molecular Theory of Hydrophobic Effects: "she is too Mean to have her Name Repeated.
-
Pratt, L. R. Molecular Theory of Hydrophobic Effects: "She is too Mean to have her Name Repeated. Annu. Rev. Phys. Chem. 2002, 53, 409-436
-
(2002)
Annu. Rev. Phys. Chem.
, vol.53
, pp. 409-436
-
-
Pratt, L.R.1
-
18
-
-
26944481188
-
Interfaces and the Driving Force of Hydrophobic Assembly
-
Chandler, D. Interfaces and the Driving Force of Hydrophobic Assembly Nature 2005, 437, 640-647
-
(2005)
Nature
, vol.437
, pp. 640-647
-
-
Chandler, D.1
-
19
-
-
12344271184
-
On the Salt-Induced Stabilization of Pair and Many-Body Hydrophobic Interactions
-
Ghosh, T.; Kalra, A.; Garde, S. On the Salt-Induced Stabilization of Pair and Many-Body Hydrophobic Interactions J. Phys. Chem. B 2005, 109, 642-651
-
(2005)
J. Phys. Chem. B
, vol.109
, pp. 642-651
-
-
Ghosh, T.1
Kalra, A.2
Garde, S.3
-
20
-
-
22144481993
-
Hydrophobic Hydration from Small to Large Lengthscales: Understanding and Manipulating the Crossover
-
Rajamani, S.; Truskett, T. M.; Garde, S. Hydrophobic Hydration From Small to Large Lengthscales: Understanding and Manipulating the Crossover Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 9475-9480
-
(2005)
Proc. Natl. Acad. Sci. U.S.A.
, vol.102
, pp. 9475-9480
-
-
Rajamani, S.1
Truskett, T.M.2
Garde, S.3
-
21
-
-
33750477655
-
Inaugural Article: Recent Progress in Understanding Hydrophobic Interactions
-
Meyer, E. E.; Rosenberg, K. J.; Israelachvili, J. Inaugural Article: Recent Progress in Understanding Hydrophobic Interactions Proc. Natl. Acad. Sci. U.S.A. 2006, 103, 15739-15746
-
(2006)
Proc. Natl. Acad. Sci. U.S.A.
, vol.103
, pp. 15739-15746
-
-
Meyer, E.E.1
Rosenberg, K.J.2
Israelachvili, J.3
-
22
-
-
34247262684
-
Integral Equation Study of Hydrophobic Interaction: A Comparison between the Simple Point Charge Model for Water and a Lennard-Jones Model for Solvent
-
Tomonari, S.; Hideo, S. Integral Equation Study of Hydrophobic Interaction: A Comparison Between the Simple Point Charge Model for Water and a Lennard-Jones Model for Solvent J. Chem. Phys. 2007, 126, 144508
-
(2007)
J. Chem. Phys.
, vol.126
, pp. 144508
-
-
Tomonari, S.1
Hideo, S.2
-
23
-
-
38849196324
-
Water as an Active Constituent in Cell Biology
-
Ball, P. Water as an Active Constituent in Cell Biology Chem. Rev. 2008, 108, 74-108
-
(2008)
Chem. Rev.
, vol.108
, pp. 74-108
-
-
Ball, P.1
-
24
-
-
0035977650
-
Molecular Dynamics Study on Hydrophobic Effects in Aqueous Urea Solutions
-
Ikeguchi, M.; Nakamura, S.; Shimizu, K. Molecular Dynamics Study on Hydrophobic Effects in Aqueous Urea Solutions. J. Am. Chem. Soc. 123, 677-682.
-
J. Am. Chem. Soc.
, vol.123
, pp. 677-682
-
-
Ikeguchi, M.1
Nakamura, S.2
Shimizu, K.3
-
25
-
-
77951547846
-
Backbone Additivity in the Transfer Model of Protein Solvation
-
Hu, C. Y.; Kokubo, H.; Lynch, G. C.; Bolen, D. W.; Pettitt, B. M. Backbone Additivity in the Transfer Model of Protein Solvation Protein Sci. 2010, 19, 1011-1022
-
(2010)
Protein Sci.
, vol.19
, pp. 1011-1022
-
-
Hu, C.Y.1
Kokubo, H.2
Lynch, G.C.3
Bolen, D.W.4
Pettitt, B.M.5
-
26
-
-
79951529371
-
Peptide Conformational Preferences in Osmolyte Solutions: Transfer Free Energies of Decaalanine
-
Kokubo, H.; Hu, C. Y.; Pettitt, B. M. Peptide Conformational Preferences in Osmolyte Solutions: Transfer Free Energies of Decaalanine J. Am. Chem. Soc. 2011, 133, 1849-1858
-
(2011)
J. Am. Chem. Soc.
, vol.133
, pp. 1849-1858
-
-
Kokubo, H.1
Hu, C.Y.2
Pettitt, B.M.3
-
27
-
-
0034227795
-
Enthalpy-Entropy and Cavity Decomposition of Alkane Hydration Free Energies: Numerical Results and Implications for Theories of Hydrophobic Solvation
-
Gallicchio, E.; Kubo, M. M.; Levy, R. M. Enthalpy-Entropy and Cavity Decomposition of Alkane Hydration Free Energies: Numerical Results and Implications for Theories of Hydrophobic Solvation J. Phys. Chem. B 2000, 104, 6271-6285
-
(2000)
J. Phys. Chem. B
, vol.104
, pp. 6271-6285
-
-
Gallicchio, E.1
Kubo, M.M.2
Levy, R.M.3
-
28
-
-
33750945327
-
A Backbone-Based Theory of Protein Folding
-
Rose, G. D.; Fleming, P. J.; Banavar, J. R.; Maritan, A. A Backbone-Based Theory of Protein Folding Proc. Natl. Acad. Sci. U.S.A. 2006, 103, 16623-16633
-
(2006)
Proc. Natl. Acad. Sci. U.S.A.
, vol.103
, pp. 16623-16633
-
-
Rose, G.D.1
Fleming, P.J.2
Banavar, J.R.3
Maritan, A.4
-
29
-
-
84862614975
-
-
University of California: San Francisco, CA.
-
Case, D. A.; Amber 12; University of California: San Francisco, CA, 2012.
-
(2012)
Amber 12
-
-
Case, D.A.1
-
30
-
-
0242663237
-
A Point-Charge Force Field for Molecular Mechanics Simulations of Proteins Based on Condensed-Phase Quantum Mechanical Calculations
-
Duan, Y.; Wu, C.; Chowdhury, S.; Lee, M. C.; Xiong, G.; Zhang, W.; Yang, R.; Cieplak, P.; Luo, R.; Lee, T.; Caldwell, J.; Wang, J.; Kollman, P. A Point-Charge Force Field for Molecular Mechanics Simulations of Proteins Based on Condensed-Phase Quantum Mechanical Calculations J. Comput. Chem. 2003, 24, 1999-2012
-
(2003)
J. Comput. Chem.
, vol.24
, pp. 1999-2012
-
-
Duan, Y.1
Wu, C.2
Chowdhury, S.3
Lee, M.C.4
Xiong, G.5
Zhang, W.6
Yang, R.7
Cieplak, P.8
Luo, R.9
Lee, T.10
Caldwell, J.11
Wang, J.12
Kollman, P.13
-
31
-
-
0004016501
-
Comparison of Simple Potential Functions for Simulating Liquid Water
-
Jorgensen, W. L. Comparison of Simple Potential Functions for Simulating Liquid Water J. Chem. Phys. 1983, 79, 926-935
-
(1983)
J. Chem. Phys.
, vol.79
, pp. 926-935
-
-
Jorgensen, W.L.1
-
32
-
-
46749127364
-
Are Current Molecular Dynamics Force Fields too Helical?
-
Best, R. B.; Buchete, N.-V.; Hummer, G. Are Current Molecular Dynamics Force Fields too Helical? Biophys. J. 2008, 95, L07-L09
-
(2008)
Biophys. J.
, vol.95
-
-
Best, R.B.1
Buchete, N.-V.2
Hummer, G.3
-
33
-
-
84865758046
-
Inclusion of Many-Body Effects in the Additive CHARMM Protein CMAP Potential Results in Enhanced Cooperativity of α -Helix and β -Hairpin Formation
-
Best, R. B.; Mittal, J.; Feig, M.; MacKerell, A. D., Jr. Inclusion of Many-Body Effects in the Additive CHARMM Protein CMAP Potential Results in Enhanced Cooperativity of α -Helix and β -Hairpin Formation Biophys. J. 2012, 103, 1045-1051
-
(2012)
Biophys. J.
, vol.103
, pp. 1045-1051
-
-
Best, R.B.1
Mittal, J.2
Feig, M.3
Mackerell Jr., A.D.4
-
34
-
-
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
-
35
-
-
84865088597
-
Comparison of Secondary Structure Formation Using 10 Different Force Fields in Microsecond Molecular Dynamics Simulations
-
Cino, E. A.; Choy, W.-Y.; Karttunen, M. Comparison of Secondary Structure Formation Using 10 Different Force Fields in Microsecond Molecular Dynamics Simulations J. Chem. Theory Comput. 2012, 8, 2725-2740
-
(2012)
J. Chem. Theory Comput.
, vol.8
, pp. 2725-2740
-
-
Cino, E.A.1
Choy, W.-Y.2
Karttunen, M.3
-
36
-
-
79955574923
-
-
version 1.3r1; Schrödinger, LLC: New York.
-
The PyMOL Molecular Graphics System, version 1.3r1; Schrödinger, LLC: New York, 2010.
-
(2010)
The PyMOL Molecular Graphics System
-
-
-
37
-
-
65249157397
-
Protonate3D: Assignment of Ionization States and Hydrogen Coordinates to Macromolecular Structures
-
Labute, P. Protonate3D: Assignment of Ionization States and Hydrogen Coordinates to Macromolecular Structures Proteins 2009, 75, 187-205
-
(2009)
Proteins
, vol.75
, pp. 187-205
-
-
Labute, P.1
-
38
-
-
23944432199
-
Comparison of Efficiency and Bias of Free Energies Computed by Exponential Averaging, the Bennett Acceptance Ratio, and Thermodynamic Integration
-
Shirts, M.; Pande, V. Comparison of Efficiency and Bias of Free Energies Computed by Exponential Averaging, the Bennett Acceptance Ratio, and Thermodynamic Integration J. Chem. Phys. 2005, 122, 144107
-
(2005)
J. Chem. Phys.
, vol.122
, pp. 144107
-
-
Shirts, M.1
Pande, V.2
-
39
-
-
0000249851
-
Avoiding Singularities and Numerical Instabilities in Free-Energy Calculations Based on Molecular Simulations
-
Beutler, T. C.; Mark, A. E.; van Schaik, R. C.; Gerber, P. R.; van Gunsteren, W. F. Avoiding Singularities and Numerical Instabilities in Free-Energy Calculations Based on Molecular Simulations Chem. Phys. Lett. 1994, 222, 529-539
-
(1994)
Chem. Phys. Lett.
, vol.222
, pp. 529-539
-
-
Beutler, T.C.1
Mark, A.E.2
Van Schaik, R.C.3
Gerber, P.R.4
Van Gunsteren, W.F.5
-
40
-
-
36449002336
-
Separation-Shifted Scaling, a New Scaling Method for Lennard-Jones Interactions in Thermodynamic Integration
-
Zacharias, M.; Straatsma, T. P.; McCammon, J. A. Separation-Shifted Scaling, a New Scaling Method for Lennard-Jones Interactions in Thermodynamic Integration J. Chem. Phys. 1994, 100, 9025-9031
-
(1994)
J. Chem. Phys.
, vol.100
, pp. 9025-9031
-
-
Zacharias, M.1
Straatsma, T.P.2
McCammon, J.A.3
-
41
-
-
0030134110
-
On the Validity of Electrostatic Linear Response in Polar Solvents
-
Åqvist, J.; Hansson, T. On the Validity of Electrostatic Linear Response in Polar Solvents J. Phys. Chem. 1996, 100, 9512-9521
-
(1996)
J. Phys. Chem.
, vol.100
, pp. 9512-9521
-
-
Åqvist, J.1
Hansson, T.2
-
42
-
-
0008863560
-
Some factors in the interpretation of protein denaturation
-
Kauzmann, W. Some factors in the interpretation of protein denaturation Adv. Protein Chem. 1959, 14, 1-63
-
(1959)
Adv. Protein Chem.
, vol.14
, pp. 1-63
-
-
Kauzmann, W.1
-
43
-
-
0038519321
-
Contribution of hydrophobic interactions to the stability of the globular conformation of proteins
-
Tanford, C. Contribution of hydrophobic interactions to the stability of the globular conformation of proteins J. Am. Chem. Soc. 1962, 84, 4240-4247
-
(1962)
J. Am. Chem. Soc.
, vol.84
, pp. 4240-4247
-
-
Tanford, C.1
|