-
1
-
-
0037264009
-
Electrostatic interactions
-
In P. Bourne and H. Weissig, editors, John Wiley and Sons, Inc., New York
-
N. A. Baker and J. A. McCammon. Electrostatic interactions. In P. Bourne and H. Weissig, editors, Structural Bioinformatics, pages 427-440. John Wiley and Sons, Inc., New York, 2003.
-
(2003)
Structural Bioinformatics
, pp. 427-440
-
-
Baker, N.A.1
McCammon, J.A.2
-
2
-
-
3242877863
-
Introduction to continuum electrostatics
-
D. A. Beard, editor, volume Computational Biology. Biophysical Society, Bethesda, MD
-
M. Gilson. Introduction to continuum electrostatics. In D. A. Beard, editor, Biophysics Textbook Online, volume Computational Biology. Biophysical Society, Bethesda, MD, 2000.
-
(2000)
Biophysics Textbook Online
-
-
Gilson, M.1
-
3
-
-
1642471862
-
Implicit solvent models
-
In O. M. Becker, Jr. MacKerell, A. D., B. Roux, and M. Watanabe, editors, Marcel Dekker, New York
-
B. Roux. Implicit solvent models. In O. M. Becker, Jr. MacKerell, A. D., B. Roux, and M. Watanabe, editors, Computational Biochemistry and Biophysics, pages 133-152. Marcel Dekker, New York, 2001.
-
(2001)
Computational Biochemistry and Biophysics
, pp. 133-152
-
-
Roux, B.1
-
4
-
-
0000062094
-
Electrostatics in biomolecular structure and dynamics
-
M. E. Davis and J. A. McCammon. Electrostatics in biomolecular structure and dynamics. Chem. Rev., 94:7684-7692, 1990.
-
(1990)
Chem. Rev
, vol.94
, pp. 7684-7692
-
-
Davis, M.E.1
McCammon, J.A.2
-
5
-
-
0029016182
-
Classical electrostatics in biology and chemistry
-
B. Honig and A. Nicholls. Classical electrostatics in biology and chemistry. Science, 268(5214):1144-9, 1995.
-
(1995)
Science
, vol.268
, Issue.5214
, pp. 1144-1149
-
-
Honig, B.1
Nicholls, A.2
-
6
-
-
1642464809
-
Poisson-boltzmann methods for biomolecular electrostatics
-
N. A. Baker. Poisson-boltzmann methods for biomolecular electrostatics. Meth. Enzymol., 383:94-118, 2004.
-
(2004)
Meth. Enzymol
, vol.383
, pp. 94-118
-
-
Baker, N.A.1
-
7
-
-
0003779959
-
-
editors, Kluwer Academic Publishers, Boston
-
Christian Holm, Patrick Kekicheff, and Rudolf Podgornik, editors. Electrostatic effects in soft matter and biophysics, volume 46 of NATO Science Series. Kluwer Academic Publishers, Boston, 2001.
-
(2001)
Electrostatic Effects In Soft Matter and Biophysics, Volume 46 of NATO Science Series
-
-
Holm, C.1
Kekicheff, P.2
Podgornik, R.3
-
8
-
-
0343791148
-
Electric moments of molecules in liquids
-
L. Onsager. Electric moments of molecules in liquids. J. Amer. Chem. Soc., 58:1486-1493, 1936.
-
(1936)
J. Amer. Chem. Soc
, vol.58
, pp. 1486-1493
-
-
Onsager, L.1
-
9
-
-
84946893847
-
Electrostatic interaction of a solute with a continuum. A direct utilization of ab initio molecular potentials for the prevision of solvent effects
-
S. Miertus, E. Scrocco, and J. Tomasi. Electrostatic interaction of a solute with a continuum. A direct utilization of ab initio molecular potentials for the prevision of solvent effects. Chem. Phys., 55:117-129, 1981.
-
(1981)
Chem. Phys
, vol.55
, pp. 117-129
-
-
Miertus, S.1
Scrocco, E.2
Tomasi, J.3
-
10
-
-
11744256643
-
Molecular interactions in solution: An overview of methods based on continuous distributions of solvent
-
J. Tomasi and M. Persico. Molecular interactions in solution: an overview of methods based on continuous distributions of solvent. Chem. Rev., 94:2027-2094, 1994.
-
(1994)
Chem. Rev
, vol.94
, pp. 2027-2094
-
-
Tomasi, J.1
Persico, M.2
-
11
-
-
84962463447
-
Thirty years of continuum solvation chemistry: A review, and prospects for the near future
-
J. Tomasi. Thirty years of continuum solvation chemistry: a review, and prospects for the near future. Theor. Chem. Acc., 112:184-203, 2004.
-
(2004)
Theor. Chem. Acc
, vol.112
, pp. 184-203
-
-
Tomasi, J.1
-
12
-
-
33751500123
-
Absolute pKa calculations with continuum dielectric methods
-
C. Lim, D. Bashford, and M. Karplus. Absolute pKa calculations with continuum dielectric methods. J. Phys. Chem., 95:5610-5620, 1991.
-
(1991)
J. Phys. Chem
, vol.95
, pp. 5610-5620
-
-
Lim, C.1
Bashford, D.2
Karplus, M.3
-
13
-
-
84962440579
-
Incorporating solvation effects into density functional theory: Calculation of absolute acidities
-
W.H. Richardson, C. Peng, D. Bashford, L. Noodleman, and D.A. Case. Incorporating solvation effects into density functional theory: Calculation of absolute acidities. Int. J. Quantum Chem., 61:207-217, 1997.
-
(1997)
Int. J. Quantum Chem
, vol.61
, pp. 207-217
-
-
Richardson, W.H.1
Peng, C.2
Bashford, D.3
Noodleman, L.4
Case, D.A.5
-
14
-
-
0037149134
-
Accurate prediction of acidity constants in aqueous solution via density functional theory and selfconsistent reaction field methods
-
J.J. Klicic, R.A. Friesner, S.Y. Liu, and W.C. Guida. Accurate prediction of acidity constants in aqueous solution via density functional theory and selfconsistent reaction field methods. J. Phys. Chem. A, 106:1327-1335, 2002.
-
(2002)
J. Phys. Chem. A
, vol.106
, pp. 1327-1335
-
-
Klicic, J.J.1
Friesner, R.A.2
Liu, S.Y.3
Guida, W.C.4
-
15
-
-
0037104738
-
Computation of pKa from Dielectric Continuum Theory
-
D.M. Chipman. Computation of pKa from Dielectric Continuum Theory. J. Phys. Chem. A, 106:7413-7422, 2002.
-
(2002)
J. Phys. Chem. A
, vol.106
, pp. 7413-7422
-
-
Chipman, D.M.1
-
16
-
-
84962450101
-
Accurate pKa Determination for a Heterogeneous Group of Organic Molecules
-
M.S. Busch and E.W. Knapp. Accurate pKa Determination for a Heterogeneous Group of Organic Molecules. Chemphyschem, 5:1513-1522, 2004.
-
(2004)
Chemphyschem
, vol.5
, pp. 1513-1522
-
-
Busch, M.S.1
Knapp, E.W.2
-
17
-
-
32844457567
-
Accurate calculation of hydration free energies using macroscopic solvent models
-
D. Sitkoff, K.A. Sharp, and B. Honig. Accurate calculation of hydration free energies using macroscopic solvent models. J. Phys. Chem., 98:1978-1988, 1994.
-
(1994)
J. Phys. Chem
, vol.98
, pp. 1978-1988
-
-
Sitkoff, D.1
Sharp, K.A.2
Honig, B.3
-
18
-
-
0031167555
-
Atomic radii for continuum electrostatics calculations based on molecular dynamics free energy simulations
-
M. Nina, D. Beglov, and B. Roux. Atomic radii for continuum electrostatics calculations based on molecular dynamics free energy simulations. J. Phys. Chem. B, 101:5239-5248, 1997.
-
(1997)
J. Phys. Chem. B
, vol.101
, pp. 5239-5248
-
-
Nina, M.1
Beglov, D.2
Roux, B.3
-
19
-
-
0037089017
-
The SGB/NP Hydration Free Energy Model Based on the Surface Generalized Born Solvent Reaction Field and Novel Nonpolar Hydration Free Energy Estimators
-
E. Gallicchio, L.Y. Zhang, and R.M. Levy. The SGB/NP Hydration Free Energy Model Based on the Surface Generalized Born Solvent Reaction Field and Novel Nonpolar Hydration Free Energy Estimators. J. Comput. Chem., 23:517-529, 2002.
-
(2002)
J. Comput. Chem
, vol.23
, pp. 517-529
-
-
Gallicchio, E.1
Zhang, L.Y.2
Levy, R.M.3
-
20
-
-
1442330396
-
AGBNP: An Analytic Implicit Solvent Model Suitable for Molecular Dynamics Simulations and High-Resolution Modeling
-
E. Gallicchio and R.M. Levy. AGBNP: An Analytic Implicit Solvent Model Suitable for Molecular Dynamics Simulations and High-Resolution Modeling. J. Comput. Chem., 25:479-499, 2004.
-
(2004)
J. Comput. Chem
, vol.25
, pp. 479-499
-
-
Gallicchio, E.1
Levy, R.M.2
-
21
-
-
34250928962
-
Volumen und hydratationswärme der ionen
-
M. Born. Volumen und hydratationswärme der ionen. Z. Phys., 1:45-48, 1920.
-
(1920)
Z. Phys
, vol.1
, pp. 45-48
-
-
Born, M.1
-
23
-
-
33947468892
-
Theory of protein titration curves. I. General equations for impenetrable spheres
-
C. Tanford and J. G. Kirkwood. Theory of protein titration curves. I. General equations for impenetrable spheres. J. Am. Chem. Soc., 79:5333-5339, 1957.
-
(1957)
J. Am. Chem. Soc
, vol.79
, pp. 5333-5339
-
-
Tanford, C.1
Kirkwood, J.G.2
-
24
-
-
0019808548
-
Electrostatic contributions to the energetics of dimer-tetramer assembly in human hemoglobin: PH dependence and effect of specifically bound chloride ions
-
M. A. Flanagan, G. K. Ackers, J. B. Matthew, G. I. H. Hanania, and F. R. N. Gurd. Electrostatic contributions to the energetics of dimer-tetramer assembly in human hemoglobin: pH dependence and effect of specifically bound chloride ions. Biochemistry, 20:7439-7449, 1981.
-
(1981)
Biochemistry
, vol.20
, pp. 7439-7449
-
-
Flanagan, M.A.1
Ackers, G.K.2
Matthew, J.B.3
Hanania, G.I.H.4
Gurd, F.R.N.5
-
25
-
-
0020475509
-
Calculation of the electric potential in the active site cleft due to alpha-helix dipoles
-
J. Warwicker and H. C. Watson. Calculation of the electric potential in the active site cleft due to alpha-helix dipoles. J. Mol. Biol., 157(4):671-9, 1982.
-
(1982)
J. Mol. Biol
, vol.157
, Issue.4
, pp. 671-679
-
-
Warwicker, J.1
Watson, H.C.2
-
26
-
-
0030852818
-
Thermodynamics of a reverse turn motif. Solvent effects and side-chain packing
-
E. Demchuk, D. Bashford, G. Gippert, and D.A. Case. Thermodynamics of a reverse turn motif. Solvent effects and side-chain packing. J. Mol. Biol., 270:305-317, 1997.
-
(1997)
J. Mol. Biol
, vol.270
, pp. 305-317
-
-
Demchuk, E.1
Bashford, D.2
Gippert, G.3
Case, D.A.4
-
27
-
-
0032560959
-
Continuum Solvent Studies of the Stability of DNA, RNA, and Phosphoramidate-DNA Helices
-
J. Srinivasan, T.E. Cheatham, III, P. Kollman, and D.A. Case. Continuum Solvent Studies of the Stability of DNA, RNA, and Phosphoramidate-DNA Helices. J. Am. Chem. Soc., 120:9401-9409, 1998.
-
(1998)
J. Am. Chem. Soc
, vol.120
, pp. 9401-9409
-
-
Srinivasan, J.1
Cheatham, T.E.2
Kollman, P.3
Case, D.A.4
-
28
-
-
0034521981
-
Calculating Structures and Free Energies of Complex Molecules: Combining Molecular Mechanics and Continuum Models
-
P.A. Kollman, I. Massova, C. Reyes, B. Kuhn, S. Huo, L. Chong, M. Lee, T. Lee, Y. Duan, W. Wang, O. Donini, P. Cieplak, J. Srinivasan, D.A. Case, and T.E. Cheatham, III. Calculating Structures and Free Energies of Complex Molecules: Combining Molecular Mechanics and Continuum Models. Accts. Chem. Res., 33:889-897, 2000.
-
(2000)
Accts. Chem. Res
, vol.33
, pp. 889-897
-
-
Kollman, P.A.1
Massova, I.2
Reyes, C.3
Kuhn, B.4
Huo, S.5
Chong, L.6
Lee, M.7
Lee, T.8
Duan, Y.9
Wang, W.10
Donini, O.11
Cieplak, P.12
Srinivasan, J.13
Case, D.A.14
Cheatham, T.E.15
-
30
-
-
0004179874
-
-
John Wiley and Sons, New York, 2nd edition
-
John David Jackson. Classical Electrodynamics. John Wiley and Sons, New York, 2nd edition, 1975.
-
(1975)
Classical Electrodynamics
-
-
Jackson, J.D.1
-
32
-
-
0015222647
-
The interpretation of protein structures: Estimation of static accessibility
-
B. Lee and F. M. Richards. The interpretation of protein structures: estimation of static accessibility. J. Mol. Biol., 55(3):379-400, 1971.
-
(1971)
J. Mol. Biol
, vol.55
, Issue.3
, pp. 379-400
-
-
Lee, B.1
Richards, F.M.2
-
33
-
-
0027159949
-
The molecular surface package
-
M. L. Connolly. The molecular surface package. J. Mol. Graph., 11(2):139-41, 1993.
-
(1993)
J. Mol. Graph
, vol.11
, Issue.2
, pp. 139-141
-
-
Connolly, M.L.1
-
34
-
-
0032096837
-
Continuum solvation model: Electrostatic forces from numerical solutions to the Poisson-Boltzmann equation
-
W. Im, D. Beglov, and B. Roux. Continuum solvation model: electrostatic forces from numerical solutions to the Poisson-Boltzmann equation. Comp. Phys. Commun., 111(1-3):59-75, 1998.
-
(1998)
Comp. Phys. Commun
, vol.111
, Issue.1-3
, pp. 59-75
-
-
Im, W.1
Beglov, D.2
Roux, B.3
-
35
-
-
0035971738
-
A smooth permittivity function for Poisson-Boltzmann solvation methods
-
J. Andrew Grant, Barry T. Pickup, and Anthony Nicholls. A smooth permittivity function for Poisson-Boltzmann solvation methods. J. Comput. Chem., 22(6):608-640, 2001.
-
(2001)
J. Comput. Chem
, vol.22
, Issue.6
, pp. 608-640
-
-
Andrew Grant, J.1
Barry, T.P.2
Nicholls, A.3
-
36
-
-
0032968444
-
Optimized atomic radii for protein continuum electrostatics solvation forces
-
M. Nina, W. Im, and B. Roux. Optimized atomic radii for protein continuum electrostatics solvation forces. Biophys. Chem., 78(1/2):89-96, 1999.
-
(1999)
Biophys. Chem
, vol.78
, Issue.1-2
, pp. 89-96
-
-
Nina, M.1
Im, W.2
Roux, B.3
-
37
-
-
0038650855
-
Comparison of calculation and experiment implicates significant electrostatic contributions to the binding stability of barnase and barstar
-
F. Dong, M. Vijaykumar, and H. X. Zhou. Comparison of calculation and experiment implicates significant electrostatic contributions to the binding stability of barnase and barstar. Biophys. J., 85(1):49-60, 2003.
-
(2003)
Biophys. J
, vol.85
, Issue.1
, pp. 49-60
-
-
Dong, F.1
Vijaykumar, M.2
Zhou, H.X.3
-
38
-
-
4444323489
-
Solvation forces on biomolecular structures: A comparison of explicit solvent and Poisson-Boltzmann models
-
J. Wagoner and N. A. Baker. Solvation forces on biomolecular structures: A comparison of explicit solvent and Poisson-Boltzmann models. J. Comput. Chem., 25(13):1623-9, 2004.
-
(2004)
J. Comput. Chem
, vol.25
, Issue.13
, pp. 1623-1629
-
-
Wagoner, J.1
Baker, N.A.2
-
39
-
-
33751552991
-
Calculating total electrostatic energies with the nonlinear Poisson-Boltzmann equation
-
K. A. Sharp and B. Honig. Calculating total electrostatic energies with the nonlinear Poisson-Boltzmann equation. J. Phys. Chem., 94(19):7684-7692, 1990.
-
(1990)
J. Phys. Chem
, vol.94
, Issue.19
, pp. 7684-7692
-
-
Sharp, K.A.1
Honig, B.2
-
40
-
-
0031578985
-
On the variational approach to Poisson-Boltzmann free energies
-
F. Fogolari and J. M. Briggs. On the variational approach to Poisson-Boltzmann free energies. Chemical Physics Letters, 281(1-3):135-139, 1997.
-
(1997)
Chemical Physics Letters
, vol.281
, Issue.1-3
, pp. 135-139
-
-
Fogolari, F.1
Briggs, J.M.2
-
41
-
-
0031572118
-
Numerical considerations in the computation of the electrostatic free energy of interaction within the Poisson-Boltzmann theory
-
A. M. Micu, B. Bagheri, A. V. Ilin, L. R. Scott, and B. M. Pettitt. Numerical considerations in the computation of the electrostatic free energy of interaction within the Poisson-Boltzmann theory. J. Comput. Phys., 136(2):263-271, 1997.
-
(1997)
J. Comput. Phys
, vol.136
, Issue.2
, pp. 263-271
-
-
Micu, A.M.1
Bagheri, B.2
Ilin, A.V.3
Scott, L.R.4
Pettitt, B.M.5
-
42
-
-
0001585447
-
Computation of electrostatic forces on solvated molecules using the Poisson-Boltzmann equation
-
M. K. Gilson, M. E. Davis, B. A. Luty, and J. A. McCammon. Computation of electrostatic forces on solvated molecules using the Poisson-Boltzmann equation. J. Phys. Chem., 97(14):3591-3600, 1993.
-
(1993)
J. Phys. Chem
, vol.97
, Issue.14
, pp. 3591-3600
-
-
Gilson, M.K.1
Davis, M.E.2
Luty, B.A.3
McCammon, J.A.4
-
43
-
-
0000105585
-
Solvation of complex molecules in a polar liquid: An integral equation theory
-
D. Beglov and B. Roux. Solvation of complex molecules in a polar liquid: an integral equation theory. J. Chem. Phys., 104(21):8678-8689, 1996.
-
(1996)
J. Chem. Phys
, vol.104
, Issue.21
, pp. 8678-8689
-
-
Beglov, D.1
Roux, B.2
-
44
-
-
0037327061
-
Continuum description of solvent dielectrics in molecular-dynamics simulations of proteins
-
B. Egwolf and P. Tavan. Continuum description of solvent dielectrics in molecular-dynamics simulations of proteins. J. Chem. Phys., 118(5):2039-56, 2003.
-
(2003)
J. Chem. Phys
, vol.118
, Issue.5
, pp. 2039-2056
-
-
Egwolf, B.1
Tavan, P.2
-
45
-
-
1242287118
-
Continuum description of ionic and dielectric shielding for molecular-dynamics simulations of proteins in solution
-
B. Egwolf and P. Tavan. Continuum description of ionic and dielectric shielding for molecular-dynamics simulations of proteins in solution. J. Chem. Phys., 120(4):2056-2068, 2004.
-
(2004)
J. Chem. Phys
, vol.120
, Issue.4
, pp. 2056-2068
-
-
Egwolf, B.1
Tavan, P.2
-
46
-
-
0000525721
-
Multigrid solution of the Poisson-Boltzmann equation
-
M. Holst and F. Saied. Multigrid solution of the Poisson-Boltzmann equation. J. Comput. Chem., 14(1):105-13, 1993.
-
(1993)
J. Comput. Chem
, vol.14
, Issue.1
, pp. 105-113
-
-
Holst, M.1
Saied, F.2
-
47
-
-
84986437211
-
Numerical solution of the nonlinear Poisson-Boltzmann equation: Developing more robust and efficient methods
-
M. J. Holst and F. Saied. Numerical solution of the nonlinear Poisson-Boltzmann equation: developing more robust and efficient methods. J. Comput. Chem., 16(3):337-64, 1995.
-
(1995)
J. Comput. Chem
, vol.16
, Issue.3
, pp. 337-364
-
-
Holst, M.J.1
Saied, F.2
-
49
-
-
0013252548
-
Finite Element Solution of Boundary Value Problems
-
Academic Press, Inc., San Diego
-
O. Axelsson and V. A. Barker. Finite Element Solution of Boundary Value Problems. Theory and Computation. Academic Press, Inc., San Diego, 1984.
-
(1984)
Theory and Computation
-
-
Axelsson, O.1
Barker, V.A.2
-
50
-
-
0035566962
-
Adaptive numerical treatment of elliptic systems on manifolds
-
M. Holst. Adaptive numerical treatment of elliptic systems on manifolds. Advances in Computational Mathematics, 15(1-4):139-191, 2001.
-
(2001)
Advances In Computational Mathematics
, vol.15
, Issue.1-4
, pp. 139-191
-
-
Holst, M.1
-
51
-
-
0000486193
-
Adaptive multilevel finite element solution of the Poisson-Boltzmann equation. I. Algorithms and examples
-
M. Holst, N. Baker, and F. Wang. Adaptive multilevel finite element solution of the Poisson-Boltzmann equation. I. Algorithms and examples. J. Comput. Chem., 21(15):1319-1342, 2000.
-
(2000)
J. Comput. Chem
, vol.21
, Issue.15
, pp. 1319-1342
-
-
Holst, M.1
Baker, N.2
Wang, F.3
-
52
-
-
0000486194
-
Adaptive multilevel finite element solution of the Poisson-Boltzmann equation II. Refinement at solvent-accessible surfaces in biomolecular systems
-
N. Baker, M. Holst, and F. Wang. Adaptive multilevel finite element solution of the Poisson-Boltzmann equation II. Refinement at solvent-accessible surfaces in biomolecular systems. J. Comput. Chem., 21(15):1343-1352, 2000.
-
(2000)
J. Comput. Chem
, vol.21
, Issue.15
, pp. 1343-1352
-
-
Baker, N.1
Holst, M.2
Wang, F.3
-
53
-
-
0001620743
-
An automatic three-dimensional finite element mesh generation system for the Poisson-Boltzmann equation
-
C. M. Cortis and R. A. Friesner. An automatic three-dimensional finite element mesh generation system for the Poisson-Boltzmann equation. J. Comput. Chem., 18:1570-1590, 1997.
-
(1997)
J. Comput. Chem
, vol.18
, pp. 1570-1590
-
-
Cortis, C.M.1
Friesner, R.A.2
-
54
-
-
0001439211
-
Numerical solution of the Poisson-Boltzmann equation using tetrahedral finite-element meshes
-
C. M. Cortis and R. A. Friesner. Numerical solution of the Poisson-Boltzmann equation using tetrahedral finite-element meshes. J. Comput. Chem., 18:1591-1608, 1997.
-
(1997)
J. Comput. Chem
, vol.18
, pp. 1591-1608
-
-
Cortis, C.M.1
Friesner, R.A.2
-
55
-
-
0036681790
-
AdaptivenumericalmethodforPoisson-Boltzmannequation and its application
-
P. E. Dyshlovenko. AdaptivenumericalmethodforPoisson-Boltzmannequation and its application. Comp. Phys. Commun., 147:335-338, 2002.
-
(2002)
Comp. Phys. Commun
, vol.147
, pp. 335-338
-
-
Dyshlovenko, P.E.1
-
56
-
-
0034879381
-
A new paradigm for parallel adaptive meshing algorithms
-
R. E. Bank and M. Holst. A new paradigm for parallel adaptive meshing algorithms. SIAM Journal on Scientific Computing, 22(4):1411-1443, 2000.
-
(2000)
SIAM Journal On Scientific Computing
, vol.22
, Issue.4
, pp. 1411-1443
-
-
Bank, R.E.1
Holst, M.2
-
57
-
-
0035327566
-
The adaptive multilevel finite element solution of the Poisson-Boltzmann equation on massively parallel computers
-
N. A. Baker, D. Sept, M. J. Holst, and J. A. McCammon. The adaptive multilevel finite element solution of the Poisson-Boltzmann equation on massively parallel computers. IBM Journal of Research and Development, 45(3/4):427-438, 2001.
-
(2001)
IBM Journal of Research and Development
, vol.45
, Issue.3-4
, pp. 427-438
-
-
Baker, N.A.1
Sept, D.2
Holst, M.J.3
McCammon, J.A.4
-
58
-
-
84988110397
-
The rigorous computation of the molecular electric potential
-
R. J. Zauhar and R. S. Morgan. The rigorous computation of the molecular electric potential. J. Comput. Chem., 9(2):171-187, 1988.
-
(1988)
J. Comput. Chem
, vol.9
, Issue.2
, pp. 171-187
-
-
Zauhar, R.J.1
Morgan, R.S.2
-
59
-
-
0002334742
-
The electric potential of a macromolecule in a solvent: A fundamental approach
-
A. H. Juffer, E. F. F. Botta, B. A. M. van Keulen, A. van der Ploeg, and H. J. C. Berendsen. The electric potential of a macromolecule in a solvent: a fundamental approach. J. Comput. Phys., 97:144-171, 1991.
-
(1991)
J. Comput. Phys
, vol.97
, pp. 144-171
-
-
Juffer, A.H.1
Botta, E.F.F.2
van Keulen, B.A.M.3
van der Ploeg, A.4
Berendsen, H.J.C.5
-
60
-
-
0029059973
-
Modeling the electrophoresis of rigid polyions: Application to lysozyme
-
S. A. Allison and V. T. Tran. Modeling the electrophoresis of rigid polyions: application to lysozyme. Biophys. J., 68(6):2261-70, 1995.
-
(1995)
Biophys. J
, vol.68
, Issue.6
, pp. 2261-2270
-
-
Allison, S.A.1
Tran, V.T.2
-
61
-
-
0037328258
-
Boundary element solution of the linear Poisson-Boltzmann equation and a multipole method for the rapid calculation of forces on macromolecules in solution
-
A. J. Bordner and G. A. Huber. Boundary element solution of the linear Poisson-Boltzmann equation and a multipole method for the rapid calculation of forces on macromolecules in solution. J. Comput. Chem., 24:353-367, 2003.
-
(2003)
J. Comput. Chem
, vol.24
, pp. 353-367
-
-
Bordner, A.J.1
Huber, G.A.2
-
62
-
-
2342454337
-
Hybrid boundary element and finite difference method for solving the nonlinear Poisson-Boltzmann equation
-
A. H. Boschitsch and M. O. Fenley. Hybrid boundary element and finite difference method for solving the nonlinear Poisson-Boltzmann equation. J. Comput. Chem., 25(7):935-955, 2004.
-
(2004)
J. Comput. Chem
, vol.25
, Issue.7
, pp. 935-955
-
-
Boschitsch, A.H.1
Fenley, M.O.2
-
63
-
-
85033849708
-
Finite-difference solution of the Poisson-Boltzmann equation: Complete elimination of selfenergy
-
Z. Zhou, P. Payne, M. Vasquez, N. Kuhn, and M. Levitt. Finite-difference solution of the Poisson-Boltzmann equation: complete elimination of selfenergy. J. Comput. Chem., 17:1344-1351, 1996.
-
(1996)
J. Comput. Chem
, vol.17
, pp. 1344-1351
-
-
Zhou, Z.1
Payne, P.2
Vasquez, M.3
Kuhn, N.4
Levitt, M.5
-
64
-
-
0001445346
-
A fast adaptive multigrid boundary element method for macromolecular electrostatic computations in a solvent
-
Y. N. Vorobjev and H. A. Scheraga. A fast adaptive multigrid boundary element method for macromolecular electrostatic computations in a solvent. J. Comput. Chem., 18(4):569-583, 1997.
-
(1997)
J. Comput. Chem
, vol.18
, Issue.4
, pp. 569-583
-
-
Vorobjev, Y.N.1
Scheraga, H.A.2
-
65
-
-
84986486656
-
A rapid finite difference algorithm, utilizing successive over-relaxation to solve the Poisson-Boltzmann equation
-
A. Nicholls and B. Honig. A rapid finite difference algorithm, utilizing successive over-relaxation to solve the Poisson-Boltzmann equation. J. Comput. Chem., 12(4):435-445, 1991.
-
(1991)
J. Comput. Chem
, vol.12
, Issue.4
, pp. 435-445
-
-
Nicholls, A.1
Honig, B.2
-
66
-
-
84988141840
-
Solving the finite difference linearized Poisson-Poltzmann equation: A comparison of relaxation and conjugate gradient methods
-
M. E. Davis and J. A. McCammon. Solving the finite difference linearized Poisson-Poltzmann equation: a comparison of relaxation and conjugate gradient methods. J. Comput. Chem., 10:386-391, 1989.
-
(1989)
J. Comput. Chem
, vol.10
, pp. 386-391
-
-
Davis, M.E.1
McCammon, J.A.2
-
67
-
-
0035964342
-
Electrostatics of nanosystems: Application to microtubules and the ribosome
-
N. A. Baker, D. Sept, S. Joseph, M. J. Holst, and J. A. McCammon. Electrostatics of nanosystems: Application to microtubules and the ribosome. Proc Natl. Acad. Sci. USA, 98(18):10037-10041, 2001.
-
(2001)
Proc Natl. Acad. Sci. USA
, vol.98
, Issue.18
, pp. 10037-10041
-
-
Baker, N.A.1
Sept, D.2
Joseph, S.3
Holst, M.J.4
McCammon, J.A.5
-
68
-
-
0023280069
-
Calculation of electrostatic potentials in an enzyme active site
-
M. K. Gilson and B. H. Honig. Calculation of electrostatic potentials in an enzyme active site. Nature, 330(6143):84-6, 1987.
-
(1987)
Nature
, vol.330
, Issue.6143
, pp. 84-86
-
-
Gilson, M.K.1
Honig, B.H.2
-
69
-
-
0025283002
-
Electrostatic interactions in macromolecules theory and applications
-
K. A. Sharp and B. Honig. Electrostatic interactions in macromolecules theory and applications. Annu. Rev. Biophys. Biophys. Chem., 19:301-332, 1990.
-
(1990)
Annu. Rev. Biophys. Biophys. Chem
, vol.19
, pp. 301-332
-
-
Sharp, K.A.1
Honig, B.2
-
70
-
-
0037142983
-
A finite difference domain decomposition method using local corrections for the solution of Poisson's equation
-
G. T. Balls and P. Colella. A finite difference domain decomposition method using local corrections for the solution of Poisson's equation. J. Comput. Phys., 180(1):25-53, 2002.
-
(2002)
J. Comput. Phys
, vol.180
, Issue.1
, pp. 25-53
-
-
Balls, G.T.1
Colella, P.2
-
71
-
-
0037080244
-
Rapid grid-based construction of the molecular surface and the use of induced surface charge to calculate reaction field energies: Applications to the molecular systems and geometric objects
-
W. Rocchia, S. Sridharan, A. Nicholls, E. Alexov, A. Chiabrera, and B. Honig. Rapid grid-based construction of the molecular surface and the use of induced surface charge to calculate reaction field energies: applications to the molecular systems and geometric objects. J. Comput. Chem., 23(1):128-37, 2002.
-
(2002)
J. Comput. Chem
, vol.23
, Issue.1
, pp. 128-137
-
-
Rocchia, W.1
Sridharan, S.2
Nicholls, A.3
Alexov, E.4
Chiabrera, A.5
Honig, B.6
-
72
-
-
0026319199
-
Protein folding and association: Insights from the interfacial and thermodynamic properties of hydrocarbons
-
A. Nicholls, K. A. Sharp, and B. Honig. Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins, 11(4):281-96, 1991.
-
(1991)
Proteins
, vol.11
, Issue.4
, pp. 281-296
-
-
Nicholls, A.1
Sharp, K.A.2
Honig, B.3
-
73
-
-
84957665033
-
An object-oriented programming suite for electrostatic effects in biological molecules
-
In Y. Ishikawa, R. R. Oldehoeft, J. V. W. Reynders, and M. Tholburn, editors, Springer, Berlin
-
D. Bashford. An object-oriented programming suite for electrostatic effects in biological molecules. In Y. Ishikawa, R. R. Oldehoeft, J. V. W. Reynders, and M. Tholburn, editors, Scientific Computing in Object-Oriented Parallel Environments, volume 1343 of Lecture Notes in Computer Science, pages 233-240. Springer, Berlin, 1997.
-
(1997)
Scientific Computing In Object-Oriented Parallel Environments, Volume 1343 of Lecture Notes In Computer Science
, pp. 233-240
-
-
Bashford, D.1
-
74
-
-
0029633152
-
Electrostatics and diffusion of molecules in solution simulations with the university of houston brownian dynamics program
-
J. D. Madura, J. M. Briggs, R. C. Wade, M. E. Davis, B. A. Luty, A. Ilin, J. Antosiewicz, M. K. Gilson, B. Bagheri, L. R. Scott, and J. A. McCammon. Electrostatics and diffusion of molecules in solution simulations with the university of houston brownian dynamics program. Comp. Phys. Commun., 91(1-3):57-95, 1995.
-
(1995)
Comp. Phys. Commun
, vol.91
, Issue.1-3
, pp. 57-95
-
-
Madura, J.D.1
Briggs, J.M.2
Wade, R.C.3
Davis, M.E.4
Luty, B.A.5
Ilin, A.6
Antosiewicz, J.7
Gilson, M.K.8
Bagheri, B.9
Scott, L.R.10
McCammon, J.A.11
-
75
-
-
0000224283
-
Charmm: The energy function and its parameterization with an overview of the program
-
In P. v. R. Schleyer, editor, John Wiley and Sons, Chichester
-
Jr. MacKerell, A. D., B. Brooks, Brooks, C. L., L. Nilsson, B. Roux, Y. Won, and M. Karplus. Charmm: the energy function and its parameterization with an overview of the program. In P. v. R. Schleyer, editor, The Encyclopedia of Computational Chemistry, volume 1, pages 271-277. John Wiley and Sons, Chichester, 1998.
-
(1998)
The Encyclopedia of Computational Chemistry
, vol.1
, pp. 271-277
-
-
Mackerell, A.D.1
Brooks, B.2
Brooks, C.L.3
Nilsson, L.4
Roux, B.5
Won, Y.6
Karplus, M.7
-
76
-
-
0036771626
-
Accelerated Poisson-Boltzmann calculations for static and dynamic systems
-
R. Luo, L. David, and M. K. Gilson. Accelerated Poisson-Boltzmann calculations for static and dynamic systems. J. Comput. Chem., 23(13):1244-53, 2002.
-
(2002)
J. Comput. Chem
, vol.23
, Issue.13
, pp. 1244-1253
-
-
Luo, R.1
David, L.2
Gilson, M.K.3
-
77
-
-
0344778061
-
Semianalytical treatement of solvation for molecular mechanics and dynamics
-
W.C. Still, A. Tempczyk, R.C. Hawley, and T. Hendrickson. Semianalytical treatement of solvation for molecular mechanics and dynamics. J. Am. Chem. Soc., 112:6127-6129, 1990.
-
(1990)
J. Am. Chem. Soc
, vol.112
, pp. 6127-6129
-
-
Still, W.C.1
Tempczyk, A.2
Hawley, R.C.3
Hendrickson, T.4
-
78
-
-
0037110472
-
Effective Born radii in the generalized Born approximation: The importance of being perfect
-
A. Onufriev, D.A. Case, and D. Bashford. Effective Born radii in the generalized Born approximation: The importance of being perfect. J. Comput. Chem., 23:1297-1304, 2002.
-
(2002)
J. Comput. Chem
, vol.23
, pp. 1297-1304
-
-
Onufriev, A.1
Case, D.A.2
Bashford, D.3
-
80
-
-
0031248940
-
Continuum Electrostatic Energies of Macromolecules in Aqueous Solutions
-
M. Scarsi, J. Apostolakis, and A. Caflisch. Continuum Electrostatic Energies of Macromolecules in Aqueous Solutions. J. Phys. Chem. A, 101:8098-8106, 1997.
-
(1997)
J. Phys. Chem. A
, vol.101
, pp. 8098-8106
-
-
Scarsi, M.1
Apostolakis, J.2
Caflisch, A.3
-
81
-
-
0037157693
-
Novel generalized Born methods
-
M.S. Lee, F.R. Salsbury, C.L. Brooks, III. Novel generalized Born methods. J. Chem. Phys., 116:10606-10614, 2002.
-
(2002)
J. Chem. Phys
, vol.116
, pp. 10606-10614
-
-
Lee, M.S.1
Salsbury, F.R.2
Brooks III, C.L.3
-
82
-
-
0038792211
-
New Analytic Approximation to the Standard Molecular Volume Definition and Its Application to Generalized Born Calculations
-
M.S. Lee, M. Feig, F.R. Salsbury, and C.L. Brooks. New Analytic Approximation to the Standard Molecular Volume Definition and Its Application to Generalized Born Calculations. J. Comput. Chem., 24:1348-1356, 2003.
-
(2003)
J. Comput. Chem
, vol.24
, pp. 1348-1356
-
-
Lee, M.S.1
Feig, M.2
Salsbury, F.R.3
Brooks, C.L.4
-
83
-
-
0025661993
-
A precise analytical method for calculating the electrostatic energy of macromolecules in aqueous solution
-
M. Schaefer and C. Froemmel. A precise analytical method for calculating the electrostatic energy of macromolecules in aqueous solution. J. Mol. Biol., 216:1045-1066, 1990.
-
(1990)
J. Mol. Biol
, vol.216
, pp. 1045-1066
-
-
Schaefer, M.1
Froemmel, C.2
-
84
-
-
0002636134
-
Pairwise solute descreening of solute charges from a dielectric medium
-
G.D. Hawkins, C.J. Cramer, and D.G. Truhlar. Pairwise solute descreening of solute charges from a dielectric medium. Chem. Phys. Lett., 246:122-129, 1995.
-
(1995)
Chem. Phys. Lett
, vol.246
, pp. 122-129
-
-
Hawkins, G.D.1
Cramer, C.J.2
Truhlar, D.G.3
-
85
-
-
33748390341
-
Parametrized models of aqueous free energies of solvation based on pairwise descreening of solute atomic charges from a dielectric medium
-
G.D. Hawkins, C.J. Cramer, and D.G. Truhlar. Parametrized models of aqueous free energies of solvation based on pairwise descreening of solute atomic charges from a dielectric medium. J. Phys. Chem., 100:19824-19839, 1996.
-
(1996)
J. Phys. Chem
, vol.100
, pp. 19824-19839
-
-
Hawkins, G.D.1
Cramer, C.J.2
Truhlar, D.G.3
-
86
-
-
20644431615
-
Theory of solutions of molecules containing widely separated charges with special applications to zwitterions
-
J. G. Kirkwood. Theory of solutions of molecules containing widely separated charges with special applications to zwitterions. J. Chem. Phys., 2:351-361, 1934.
-
(1934)
J. Chem. Phys
, vol.2
, pp. 351-361
-
-
Kirkwood, J.G.1
-
87
-
-
0033654297
-
Generalized Born Models of Macromolecular Solvation Effects
-
D. Bashford and D.A. Case. Generalized Born Models of Macromolecular Solvation Effects. Annu. Rev. Phys. Chem., 51:129-152, 2000.
-
(2000)
Annu. Rev. Phys. Chem
, vol.51
, pp. 129-152
-
-
Bashford, D.1
Case, D.A.2
-
88
-
-
1942456697
-
Recent advances in the development and application of implicit solvent models in biomolecule simulations
-
M. Feig and C.L. Brooks Recent advances in the development and application of implicit solvent models in biomolecule simulations. Curr. Opin. Struct. Biol., 14:217-224, 2004.
-
(2004)
Curr. Opin. Struct. Biol
, vol.14
, pp. 217-224
-
-
Feig, M.1
Brooks, C.L.2
-
89
-
-
0346971105
-
Performance Comparison of Generalized Born and Poisson Methods in the Calculation of Electrostatic Solvation Energies for Protein Structures
-
M. Feig, A. Onufriev, M.S. Lee, W. Im, D.A. Case, and C.L. Brooks. Performance Comparison of Generalized Born and Poisson Methods in the Calculation of Electrostatic Solvation Energies for Protein Structures. J. Comput. Chem., 25:265-284, 2004.
-
(2004)
J. Comput. Chem
, vol.25
, pp. 265-284
-
-
Feig, M.1
Onufriev, A.2
Lee, M.S.3
Im, W.4
Case, D.A.5
Brooks, C.L.6
-
90
-
-
0012227656
-
A comprehensive analytical treatment of continuum electrostatics
-
M. Schaefer and M. Karplus. A comprehensive analytical treatment of continuum electrostatics. J. Phys. Chem., 100:1578-1599, 1996.
-
(1996)
J. Phys. Chem
, vol.100
, pp. 1578-1599
-
-
Schaefer, M.1
Karplus, M.2
-
91
-
-
20644449471
-
Modification of the Generalized Born Model Suitable for Macromolecules
-
A. Onufriev, D. Bashford, and D.A. Case. Modification of the Generalized Born Model Suitable for Macromolecules. J. Phys. Chem. B, 104:3712-3720, 2000.
-
(2000)
J. Phys. Chem. B
, vol.104
, pp. 3712-3720
-
-
Onufriev, A.1
Bashford, D.2
Case, D.A.3
-
92
-
-
1842479952
-
Exploring Protein Native States and Large-Scale Conformational Changes With a Modified Generalized Born Model
-
A. Onufriev, D. Bashford, and D.A. Case. Exploring Protein Native States and Large-Scale Conformational Changes With a Modified Generalized Born Model. Proteins, 55:383-394, 2004.
-
(2004)
Proteins
, vol.55
, pp. 383-394
-
-
Onufriev, A.1
Bashford, D.2
Case, D.A.3
-
93
-
-
0021107965
-
Solvent-accessible surfaces of proteins and nucleic acids
-
M.L. Connolly. Solvent-accessible surfaces of proteins and nucleic acids. Science, 221:709-713, 1983.
-
(1983)
Science
, vol.221
, pp. 709-713
-
-
Connolly, M.L.1
-
94
-
-
0001246294
-
Generalized Born Model Based on a Surface Integral Formulation
-
A. Ghosh, C.S. Rapp, and R.A. Friesner. Generalized Born Model Based on a Surface Integral Formulation. J. Phys. Chem. B, 102:10983-10990, 1998.
-
(1998)
J. Phys. Chem. B
, vol.102
, pp. 10983-10990
-
-
Ghosh, A.1
Rapp, C.S.2
Friesner, R.A.3
-
95
-
-
0035965145
-
Prediction of functionally important residues based solely on the computed energetics of protein structure
-
A. H. Elcock. Prediction of functionally important residues based solely on the computed energetics of protein structure. J. Mol. Biol., 312(4):885-896, 2001.
-
(2001)
J. Mol. Biol
, vol.312
, Issue.4
, pp. 885-896
-
-
Elcock, A.H.1
-
96
-
-
0035940421
-
Thematics: A simple computational predictor of enzyme function from structure
-
M. J. Ondrechen, J. G. Clifton, and D. Ringe. Thematics: a simple computational predictor of enzyme function from structure. Proc. Natl. Acad. Sci. USA, 98(22):12473-8, 2001.
-
(2001)
Proc. Natl. Acad. Sci. USA
, vol.98
, Issue.22
, pp. 12473-12478
-
-
Ondrechen, M.J.1
Clifton, J.G.2
Ringe, D.3
-
97
-
-
0029775624
-
Clusters of charged residues in protein threedimensional structures
-
Z. Y. Zhu and S. Karlin. Clusters of charged residues in protein threedimensional structures. Proc. Natl. Acad. Sci. USA, 93(16):8350-5, 1996.
-
(1996)
Proc. Natl. Acad. Sci. USA
, vol.93
, Issue.16
, pp. 8350-8355
-
-
Zhu, Z.Y.1
Karlin, S.2
-
98
-
-
84986467750
-
Quantitative comparison of molecular electrostatic potentials for structure-activity studies
-
A. M. Richard. Quantitative comparison of molecular electrostatic potentials for structure-activity studies. J. Comput. Chem., 12(8):959-69, 1991.
-
(1991)
J. Comput. Chem
, vol.12
, Issue.8
, pp. 959-969
-
-
Richard, A.M.1
-
99
-
-
0034769223
-
Electrostatic contributions to protein-protein interactions: Fast energetic filters for docking and their physical basis
-
R. Norel, F. Sheinerman, D. Petrey, and B. Honig. Electrostatic contributions to protein-protein interactions: Fast energetic filters for docking and their physical basis. Prot. Sci., 10(11):2147-2161, 2001.
-
(2001)
Prot. Sci
, vol.10
, Issue.11
, pp. 2147-2161
-
-
Norel, R.1
Sheinerman, F.2
Petrey, D.3
Honig, B.4
-
100
-
-
0030983121
-
Analysis of the black-eyed pea trypsin and chymotrypsin inhibitor-alpha-chymotrypsin complex
-
S. M. de Freitas, L. V. de Mello, M. C. da Silva, G. Vriend, G. Neshich, and M. M. Ventura. Analysis of the black-eyed pea trypsin and chymotrypsin inhibitor-alpha-chymotrypsin complex. FEBS Lett, 409(2):121-7, 1997.
-
(1997)
FEBS Lett
, vol.409
, Issue.2
, pp. 121-127
-
-
de Freitas, S.M.1
de Mello, L.V.2
da Silva, M.C.3
Vriend, G.4
Neshich, G.5
Ventura, M.M.6
-
101
-
-
0003187567
-
The atomic structure of protein-protein recognition sites
-
L. Lo Conte, C. Chothia, and J. Janin. The atomic structure of protein-protein recognition sites. J Mol Biol, 285(5):2177-98, 1999.
-
(1999)
J Mol Biol
, vol.285
, Issue.5
, pp. 2177-2198
-
-
Lo Conte, L.1
Chothia, C.2
Janin, J.3
-
102
-
-
0025123333
-
The structure of protein-protein recognition sites
-
J. Janin and C. Chothia. The structure of protein-protein recognition sites. J. Biol. Chem., 265(27):16027-30, 1990.
-
(1990)
J. Biol. Chem
, vol.265
, Issue.27
, pp. 16027-16030
-
-
Janin, J.1
Chothia, C.2
-
103
-
-
0025861597
-
Electrostatic orientation of the electron-transfer complex between plastocyanin and cytochrome c
-
V. A. Roberts, H. C. Freeman, A. J. Olson, J. A. Tainer, and E. D. Getzoff. Electrostatic orientation of the electron-transfer complex between plastocyanin and cytochrome c. J. Biol. Chem., 266(20):13431-41, 1991.
-
(1991)
J. Biol. Chem
, vol.266
, Issue.20
, pp. 13431-13441
-
-
Roberts, V.A.1
Freeman, H.C.2
Olson, A.J.3
Tainer, J.A.4
Getzoff, E.D.5
-
104
-
-
0035811237
-
Protein interaction property similarity analysis
-
R. C. Wade, R. R. Gabdoulline, and F. De Rienzo. Protein interaction property similarity analysis. International Journal of Quantum Chemistry, 83(3-4):122-127, 2001.
-
(2001)
International Journal of Quantum Chemistry
, vol.83
, Issue.3-4
, pp. 122-127
-
-
Wade, R.C.1
Gabdoulline, R.R.2
de Rienzo, F.3
-
105
-
-
0026438116
-
Electrostatic fields in antibodies and antibody/antigen complexes
-
J. Novotny and K. Sharp. Electrostatic fields in antibodies and antibody/antigen complexes. Prog. Biophys. Mol. Biol., 58(3):203-24, 1992.
-
(1992)
Prog. Biophys. Mol. Biol
, vol.58
, Issue.3
, pp. 203-224
-
-
Novotny, J.1
Sharp, K.2
-
106
-
-
0031547966
-
Electrostatic complementarity at protein/protein interfaces
-
A. J. McCoy, V. Chandana Epa, and P. M. Colman. Electrostatic complementarity at protein/protein interfaces. J. Mol. Biol., 268(2):570-84, 1997.
-
(1997)
J. Mol. Biol
, vol.268
, Issue.2
, pp. 570-584
-
-
McCoy, A.J.1
Chandana, E.V.2
Colman, P.M.3
-
107
-
-
0034702838
-
Membrane binding of peptides containing both basic and aromatic residues. experimental studies with peptides corresponding to the scaffolding region of caveolin and the effector region of marcks
-
A. Arbuzova, L. B. Wang, J. Y. Wang, G. Hangyas-Mihalyne, D. Murray, B. Honig, and S. McLaughlin. Membrane binding of peptides containing both basic and aromatic residues. experimental studies with peptides corresponding to the scaffolding region of caveolin and the effector region of marcks. Biochemistry, 39(33):10330-10339, 2000.
-
(2000)
Biochemistry
, vol.39
, Issue.33
, pp. 10330-10339
-
-
Arbuzova, A.1
Wang, L.B.2
Wang, J.Y.3
Hangyas-Mihalyne, G.4
Murray, D.5
Honig, B.6
McLaughlin, S.7
-
108
-
-
0036708447
-
Bridging the implicit and explicit solvent approaches for membrane electrostatics
-
Jung-Hsin Lin, Nathan Andrew Baker, and J. Andrew McCammon. Bridging the implicit and explicit solvent approaches for membrane electrostatics. Biophys. J., 83(3):1374-1379, 2002.
-
(2002)
Biophys. J
, vol.83
, Issue.3
, pp. 1374-1379
-
-
Lin, J.-H.1
Baker, N.A.2
Andrew, M.J.3
-
109
-
-
0036161583
-
Electrostatic control of the membrane targeting of C2 domains
-
D. Murray and B. Honig. Electrostatic control of the membrane targeting of C2 domains. Molecular Cell, 9(1):145-154, 2002.
-
(2002)
Molecular Cell
, vol.9
, Issue.1
, pp. 145-154
-
-
Murray, D.1
Honig, B.2
-
110
-
-
0030891436
-
Simulation of the diffusional association of barnase and barstar
-
R. R. Gabdoulline and R. C. Wade. Simulation of the diffusional association of barnase and barstar. Biophys J, 72(5):1917-29, 1997.
-
(1997)
Biophys J
, vol.72
, Issue.5
, pp. 1917-1929
-
-
Gabdoulline, R.R.1
Wade, R.C.2
-
111
-
-
36549102274
-
Brownian dynamics simulation of diffusion-influenced biomolecular reactions
-
S. H. Northrup, S. A. Allison, and J. A. McCammon. Brownian dynamics simulation of diffusion-influenced biomolecular reactions. J. Chem. Phys., 80:1517-1524, 1984.
-
(1984)
J. Chem. Phys
, vol.80
, pp. 1517-1524
-
-
Northrup, S.H.1
Allison, S.A.2
McCammon, J.A.3
-
112
-
-
0000945413
-
Conformational sampling with Poisson-Boltzmann forces and a stochastic dynamics monte carlo method: Application to alanine dipeptide
-
J. L. Smart, T. J. Marrone, and J. A. McCammon. Conformational sampling with Poisson-Boltzmann forces and a stochastic dynamics monte carlo method: Application to alanine dipeptide. J. Comput. Chem., 18(14):1750-1759, 1997.
-
(1997)
J. Comput. Chem
, vol.18
, Issue.14
, pp. 1750-1759
-
-
Smart, J.L.1
Marrone, T.J.2
McCammon, J.A.3
-
113
-
-
9244259076
-
Implementation and testing of stable, fast implicit solvation in molecular dynamics using the smooth-permittivity finite difference Poisson-Boltzmann method
-
N. V. Prabhu, P. Zhu, and K. A. Sharp. Implementation and testing of stable, fast implicit solvation in molecular dynamics using the smooth-permittivity finite difference Poisson-Boltzmann method. J. Comput. Chem., 25(16):2049-2064, 2004.
-
(2004)
J. Comput. Chem
, vol.25
, Issue.16
, pp. 2049-2064
-
-
Prabhu, N.V.1
Zhu, P.2
Sharp, K.A.3
-
114
-
-
0347410858
-
A Poisson-Boltzmann dynamics method with nonperiodic boundary condition
-
Q. Lu and R. Luo. A Poisson-Boltzmann dynamics method with nonperiodic boundary condition. J. Chem. Phys., 119(21):11035-11047, 2003.
-
(2003)
J. Chem. Phys
, vol.119
, Issue.21
, pp. 11035-11047
-
-
Lu, Q.1
Luo, R.2
-
115
-
-
0037103014
-
Protein Molecular Dynamics With Electrostatic Force Entirely Determined by a Single Poisson-Boltzmann Calculation
-
B.Z. Lu, W.Z. Chen, C.X. Wang, and X. Xu. Protein Molecular Dynamics With Electrostatic Force Entirely Determined by a Single Poisson-Boltzmann Calculation. Proteins, 48:497-504, 2002.
-
(2002)
Proteins
, vol.48
, pp. 497-504
-
-
Lu, B.Z.1
Chen, W.Z.2
Wang, C.X.3
Xu, X.4
-
116
-
-
0038650794
-
Protocol for MM/PBSA molecular dynamics simulations of proteins
-
F. Fogolari, A. Brigo, and H. Molinari. Protocol for MM/PBSA molecular dynamics simulations of proteins. Biophys. J., 85(1):159-166, 2003.
-
(2003)
Biophys. J
, vol.85
, Issue.1
, pp. 159-166
-
-
Fogolari, F.1
Brigo, A.2
Molinari, H.3
-
117
-
-
0034521981
-
Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models
-
P. A. Kollman, I. Massova, C. Reyes, B. Kuhn, S. Huo, L. Chong, M. Lee, T. Lee, Y. Duan, W. Wang, O. Donini, P. Cieplak, J. Srinivasan, D. A. Case, and III Cheatham, T. E. Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. Accounts of Chemical Research, 33(12):889-97, 2000.
-
(2000)
Accounts of Chemical Research
, vol.33
, Issue.12
, pp. 889-897
-
-
Kollman, P.A.1
Massova, I.2
Reyes, C.3
Kuhn, B.4
Huo, S.5
Chong, L.6
Lee, M.7
Lee, T.8
Duan, Y.9
Wang, W.10
Donini, O.11
Cieplak, P.12
Srinivasan, J.13
Case, D.A.14
Cheatham III, T.E.15
-
118
-
-
0347949637
-
Revisiting free energy calculations: A theoretical connection to MM/PBSA and direct calculation of the association free energy
-
J. M. J. Swanson, R. H. Henchman, and J. A. McCammon. Revisiting free energy calculations: A theoretical connection to MM/PBSA and direct calculation of the association free energy. Biophys. J., 86(1):67-74, 2004.
-
(2004)
Biophys. J
, vol.86
, Issue.1
, pp. 67-74
-
-
Swanson, J.M.J.1
Henchman, R.H.2
McCammon, J.A.3
-
119
-
-
0037305552
-
a calculations
-
J. E. Nielsen and J. A. McCammon. On the evaluation and optimization of protein x-ray structures for pKa calculations. Prot. Sci., 12(2):313-26, 2003.
-
(2003)
Prot. Sci
, vol.12
, Issue.2
, pp. 313-326
-
-
Nielsen, J.E.1
McCammon, J.A.2
-
120
-
-
0036787760
-
as in proteins
-
R. E. Georgescu, E. G. Alexov, and M. R. Gunner. Combining conformational flexibility and continuum electrostatics for calculating pKas in proteins. Biophys. J., 83(4):1731-1748, 2002.
-
(2002)
Biophys. J
, vol.83
, Issue.4
, pp. 1731-1748
-
-
Georgescu, R.E.1
Alexov, E.G.2
Gunner, M.R.3
-
121
-
-
4644264472
-
a calculations through flexibility based sampling of a water-dominated interaction scheme
-
J. Warwicker. Improved pKa calculations through flexibility based sampling of a water-dominated interaction scheme. Prot. Sci., 13(10):2793-805, 2004.
-
(2004)
Prot. Sci
, vol.13
, Issue.10
, pp. 2793-2805
-
-
Warwicker, J.1
-
124
-
-
0021782348
-
pH-dependent processes in proteins
-
J.B. Matthew, F.R.N. Gurd, B. Garcia-Moreno, M.A. Flanagan, K.L. March, and S.J. Shire. pH-dependent processes in proteins. CRC Crit. Rev. Biochem., 18:91-197, 1985.
-
(1985)
CRC Crit. Rev. Biochem
, vol.18
, pp. 91-197
-
-
Matthew, J.B.1
Gurd, F.R.N.2
Garcia-Moreno, B.3
Flanagan, M.A.4
March, K.L.5
Shire, S.J.6
-
125
-
-
0032319206
-
Calculations of proton-binding thermodynamics in proteins
-
P. Beroza and D.A. Case. Calculations of proton-binding thermodynamics in proteins. Meth. Enzymol., 295:170-189, 1998.
-
(1998)
Meth. Enzymol
, vol.295
, pp. 170-189
-
-
Beroza, P.1
Case, D.A.2
-
126
-
-
2442693239
-
Macroscopic electrostatic models for protonation states in proteins
-
D. Bashford. Macroscopic electrostatic models for protonation states in proteins. Frontiers Biosci., 9:1082-1099, 2004.
-
(2004)
Frontiers Biosci
, vol.9
, pp. 1082-1099
-
-
Bashford, D.1
-
127
-
-
1542320003
-
Structural interpretation of pH and saltdependent processes in proteins with computaional methods
-
B. García-Moreno and C.A. Fitch. Structural interpretation of pH and saltdependent processes in proteins with computaional methods. Meth. Enzymol., 380:20-51, 2004.
-
(2004)
Meth. Enzymol
, vol.380
, pp. 20-51
-
-
García-Moreno, B.1
Fitch, C.A.2
-
128
-
-
33947468892
-
Theory of titration curves. I. General equations for impenetrable spheres
-
C. Tanford and J.G. Kirkwood. Theory of titration curves. I. General equations for impenetrable spheres. J. Am. Chem. Soc., 79:5333-5339, 1957.
-
(1957)
J. Am. Chem. Soc
, vol.79
, pp. 5333-5339
-
-
Tanford, C.1
Kirkwood, J.G.2
-
129
-
-
33947461074
-
Theory of protein titration curves. II. Calculations for simple models at low ionic strength
-
C. Tanford. Theory of protein titration curves. II. Calculations for simple models at low ionic strength. J. Am. Chem. Soc., 79:5340-5347, 1957.
-
(1957)
J. Am. Chem. Soc
, vol.79
, pp. 5340-5347
-
-
Tanford, C.1
-
130
-
-
0015520587
-
Interpretation of protein titration curves
-
C. Tanford and R. Roxby. Interpretation of protein titration curves. Biochemistry, 11:2192-2198, 1972.
-
(1972)
Biochemistry
, vol.11
, pp. 2192-2198
-
-
Tanford, C.1
Roxby, R.2
-
131
-
-
0016207302
-
Electrostatic effects in myoglobin. Hydrogen ion equilibria in sperm whale ferrimyoglobin
-
S.J. Shire, G.I.H. Hanania, and F.R.N. Gurd. Electrostatic effects in myoglobin. Hydrogen ion equilibria in sperm whale ferrimyoglobin. Biochemistry, 13:2967-2974, 1974.
-
(1974)
Biochemistry
, vol.13
, pp. 2967-2974
-
-
Shire, S.J.1
Hanania, G.I.H.2
Gurd, F.R.N.3
-
132
-
-
0022522422
-
Calculation of electrostatic interactions in proteins
-
J.B. Matthew and F.R.N. Gurd. Calculation of electrostatic interactions in proteins. Meth. Enzymol., 130:413-436, 1986.
-
(1986)
Meth. Enzymol
, vol.130
, pp. 413-436
-
-
Matthew, J.B.1
Gurd, F.R.N.2
-
133
-
-
0035957234
-
A novel view of pH titration in biomolecules
-
A. Onufriev, D.A. Case, and G.M. Ullmann. A novel view of pH titration in biomolecules. Biochemistry, 40:3413-3419, 2001.
-
(2001)
Biochemistry
, vol.40
, pp. 3413-3419
-
-
Onufriev, A.1
Case, D.A.2
Ullmann, G.M.3
-
134
-
-
0038374931
-
Free energy of proton binding in proteins
-
D. Poland. Free energy of proton binding in proteins. Biopolymers, 69:60-71, 2003.
-
(2003)
Biopolymers
, vol.69
, pp. 60-71
-
-
Poland, D.1
-
135
-
-
0026095641
-
Protonation of interacting residues in a protein by Monte Carlo method: Application to lysozyme and the photosynthetic reaction center of Rhodobacter sphaeroides
-
P. Beroza, D.R. Fredkin, M.Y. Okamura, and G. Feher. Protonation of interacting residues in a protein by Monte Carlo method: Application to lysozyme and the photosynthetic reaction center of Rhodobacter sphaeroides. Proc. Natl. Acad. Sci. USA, 88:5804-5808, 1991.
-
(1991)
Proc. Natl. Acad. Sci. USA
, vol.88
, pp. 5804-5808
-
-
Beroza, P.1
Fredkin, D.R.2
Okamura, M.Y.3
Feher, G.4
-
136
-
-
0030970305
-
Simulation of protein conformational freedom as a function of pH: Constant-pH molecular dynamics using implicit titration
-
A.M. Baptista, P.J. Martel, and S.B. Petersen. Simulation of protein conformational freedom as a function of pH: Constant-pH molecular dynamics using implicit titration. Proteins, 27:523-544, 1997.
-
(1997)
Proteins
, vol.27
, pp. 523-544
-
-
Baptista, A.M.1
Martel, P.J.2
Petersen, S.B.3
-
137
-
-
0035827113
-
Explicit-solvent molecular dynamics simulation at constant pH: Methodology and application to small amines
-
U. Börjesson and P.H. Hünenberger. Explicit-solvent molecular dynamics simulation at constant pH: Methodology and application to small amines. J. Chem. Phys., 114:9706-9719, 2001.
-
(2001)
J. Chem. Phys
, vol.114
, pp. 9706-9719
-
-
Börjesson, U.1
Hünenberger, P.H.2
-
138
-
-
0036573188
-
Comment on Explicit-solvent molecular dynamics simulation at constant pH: Methodology and application to small amines
-
A.M. Baptista. Comment on "Explicit-solvent molecular dynamics simulation at constant pH: Methodology and application to small amines". J. Chem. Phys., 116:7766-7768, 2002.
-
(2002)
J. Chem. Phys
, vol.116
, pp. 7766-7768
-
-
Baptista, A.M.1
-
139
-
-
4444267747
-
pH-dependent stability of a decalysine α-helix studied by explicit-solvent molecular dynamics simulations at constant pH
-
U. Börjesson and P.H. Hünenberger. pH-dependent stability of a decalysine α-helix studied by explicit-solvent molecular dynamics simulations at constant pH. J. Phys. Chem. B, 108:13551-13559, 2004.
-
(2004)
J. Phys. Chem. B
, vol.108
, pp. 13551-13559
-
-
Börjesson, U.1
Hünenberger, P.H.2
-
140
-
-
4043132337
-
Constant-pH molecular dynamics using continuous titration coordinates
-
M.S. Lee, F.R. Salsbury, and C.L. Brooks. Constant-pH molecular dynamics using continuous titration coordinates. Proteins, 56:738-752, 2004.
-
(2004)
Proteins
, vol.56
, pp. 738-752
-
-
Lee, M.S.1
Salsbury, F.R.2
Brooks, C.L.3
-
141
-
-
0001692244
-
λ-dynamics: A new approach to free energy calculations
-
X. Kong and C.L. Brooks, λ-dynamics: A new approach to free energy calculations. J. Chem. Phys., 105:2414-2423, 1996.
-
(1996)
J. Chem. Phys
, vol.105
, pp. 2414-2423
-
-
Kong, X.1
Brooks, C.L.2
-
142
-
-
0036732086
-
Constant-pH molecular dynamics using stochastic titration
-
A.M. Baptista, V.H. Teixeira, and C.M. Soares. Constant-pH molecular dynamics using stochastic titration. J. Chem. Phys., 117:4184-4200, 2002.
-
(2002)
J. Chem. Phys
, vol.117
, pp. 4184-4200
-
-
Baptista, A.M.1
Teixeira, V.H.2
Soares, C.M.3
-
143
-
-
2942737233
-
Constant-pH molecular dynamics simulations: A test case for succinic acid
-
M. Dlugosz and J.M. Antosiewicz. Constant-pH molecular dynamics simulations: a test case for succinic acid. Chem. Phys., 302:161-170, 2004.
-
(2004)
Chem. Phys
, vol.302
, pp. 161-170
-
-
Dlugosz, M.1
Antosiewicz, J.M.2
-
144
-
-
42749101264
-
Constant-pH molecular dynamics study of protonation-structure relationship in a hexapeptide derived from ovomucoid third domain
-
M. Dlugosz, J.M. Antosiewicz, and A.D. Robertson. Constant-pH molecular dynamics study of protonation-structure relationship in a hexapeptide derived from ovomucoid third domain. Phys. Rev. E, 69:021915, 2004.
-
(2004)
Phys. Rev. E
, vol.69
, pp. 021915
-
-
Dlugosz, M.1
Antosiewicz, J.M.2
Robertson, A.D.3
-
145
-
-
9244223045
-
Constant pH molecular dynamics in generalized Born implicit solvent
-
J. Mongan, D.A. Case, and J.A. McCammon. Constant pH molecular dynamics in generalized Born implicit solvent. J. Comput. Chem., 25:2038-2048, 2004.
-
(2004)
J. Comput. Chem
, vol.25
, pp. 2038-2048
-
-
Mongan, J.1
Case, D.A.2
McCammon, J.A.3
-
146
-
-
2942700087
-
Comment on "can a continuum solvent model reproduce the free energy landscape of a-hairpin folding in water?" the poisson-boltzmann equation
-
R. Zhou, G. Krilov, and B. J. Berne. Comment on "can a continuum solvent model reproduce the free energy landscape of a-hairpin folding in water?" the poisson-boltzmann equation. J. Phys. Chem. B, 108(22):7528-30, 2004.
-
(2004)
J. Phys. Chem. B
, vol.108
, Issue.22
, pp. 7528-7530
-
-
Zhou, R.1
Krilov, G.2
Berne, B.J.3
-
147
-
-
4444323489
-
Solvation Forces on Biomolecular Structures: A Comparison of Explicit Solvent and Poisson-Boltzmann Models
-
J. Wagoner and N.A. Baker. Solvation Forces on Biomolecular Structures: A Comparison of Explicit Solvent and Poisson-Boltzmann Models. J. Comput. Chem., 25:1623-1629, 2004.
-
(2004)
J. Comput. Chem
, vol.25
, pp. 1623-1629
-
-
Wagoner, J.1
Baker, N.A.2
-
148
-
-
0032968444
-
Optimized atomic radii for protein continuum electrostatics solvations forces
-
M. Nina, W. Im, and B. Roux. Optimized atomic radii for protein continuum electrostatics solvations forces. Biophys. Chem., 78:89-96, 1999.
-
(1999)
Biophys. Chem
, vol.78
, pp. 89-96
-
-
Nina, M.1
Im, W.2
Roux, B.3
|