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New York: Cambridge University Press. [Provides descriptions of finite difference and finite element methods as well as several solution methods for partial differential equations.]
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Braess D (1997): Finite Elements. Theory, Fast Solvers, and Applications in Solid Mechanics. New York: Cambridge University Press. [Provides descriptions of finite difference and finite element methods as well as several solution methods for partial differential equations.]
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Finite Elements. Theory, Fast Solvers, and Applications in Solid Mechanics
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Braess, D.1
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Baker NA, Holst MJ, Wang F (2000): Adaptive multilevel finite element solution of the Poisson-Boltzmann equation II: refinement at solvent accessible surfaces in biomolecular systems. J Comput Chem 21:1343-52. [This article describes the application of finite element methods to the solution of the PBE.]
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J Comput Chem
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Electrostatics of cellular components: application to microtubules and the ribosome
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USA, [This article describes the efficient parallel solution of the Poisson-Boltzmann equation for large biomolecules.]
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Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA (2001a) Electrostatics of cellular components: application to microtubules and the ribosome. Proc Natl Acad Sci USA 89:10037-41. [This article describes the efficient parallel solution of the Poisson-Boltzmann equation for large biomolecules.]
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0035327566
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The adaptive multilevel finite element solution of the Poisson-Boltzmann equation on massively parallel computers
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[Both Baker et al. 2001 papers describe efficient parallel algorithms for both the finite difference and finite element solution of the PBE for biomolecular systems at the near-cellular scale.]
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Baker NA, Sept D, Holst MJ, McCammon JA (2001b) The adaptive multilevel finite element solution of the Poisson-Boltzmann equation on massively parallel computers. IBM J Res Dev 45:427-38. [Both Baker et al. 2001 papers describe efficient parallel algorithms for both the finite difference and finite element solution of the PBE for biomolecular systems at the near-cellular scale.]
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IBM J Res Dev
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Baker, N.A.1
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Volumen und hydratationswärme der ionen
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Born, M.1
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Computer simulation of protein-protein interactions
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[A review of modern methods for simulating interactions between proteins.]
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Elcock AH, Sept D, McCammon JA (2001): Computer simulation of protein-protein interactions. J Phys Chem B 105:1504-18. [A review of modern methods for simulating interactions between proteins.]
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J Phys Chem B
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Elcock, A.H.1
Sept, D.2
McCammon, J.A.3
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Brownian dynamics with hydrodynamic interactions
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[Introduced the method for simulating the diffusional motion of biopolymers or other molecules, including the effects of electrostatic interactions.]
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Ermak DL, McCammon JA (1978): Brownian dynamics with hydrodynamic interactions. J Chem Phys 69:1352-60. [Introduced the method for simulating the diffusional motion of biopolymers or other molecules, including the effects of electrostatic interactions.]
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Ermak, D.L.1
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0019808548
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Electrostatic contributions to the energetics of dimer-tetramer assembly in human hemoglobin: pH dependence and effect of specifically bound chloride ions
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[Uses the Tanford-Kirkwood model for protein titration to determine pH effects on hemoglobin dimer-tetramer assembly.]
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Flanagan MA, Ackers GK, Matthew JB, Hanania GIH, Gurd FRN (1981): Electrostatic contributions to the energetics of dimer-tetramer assembly in human hemoglobin: pH dependence and effect of specifically bound chloride ions. Biochemistry 20:7439-49. [Uses the Tanford-Kirkwood model for protein titration to determine pH effects on hemoglobin dimer-tetramer assembly.]
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Biochemistry
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Flanagan, M.A.1
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Matthew, J.B.3
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Gurd, F.R.N.5
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12
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0035830963
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Protein-protein association: investigation of factors influencing association rates by Brownian dynamics simulations
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[Provides an analysis of the diffusional encounter simulations of a variety of different pairs of proteins.]
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Gabdoulline RR, Wade RC (2001): Protein-protein association: investigation of factors influencing association rates by Brownian dynamics simulations. J Mol Biol 306:1139-55. [Provides an analysis of the diffusional encounter simulations of a variety of different pairs of proteins.]
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Gabdoulline, R.R.1
Wade, R.C.2
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0001585447
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Computation of electrostatic forces on solvated molecules using the Poisson-Boltzmann equation
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[Description of the calculation of forces from solutions to PBE.]
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Gilson MK, Davis ME, Luty B, McCammon JA (1993): Computation of electrostatic forces on solvated molecules using the Poisson-Boltzmann equation. J Phys Chem 97:3591-600. [Description of the calculation of forces from solutions to PBE.]
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J Phys Chem
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Gilson, M.K.1
Davis, M.E.2
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0000486193
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Adaptive multilevel finite element solution of the Poisson-Boltzmann equation I: algorithms and examples
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Holst MJ, Baker NA, Wang F (2000a) Adaptive multilevel finite element solution of the Poisson-Boltzmann equation I: algorithms and examples. J Comput Chem 21:1319-42.
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J Comput Chem
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Wang, F.3
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84986437211
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Numerical solution of the nonlinear Poisson-Boltzmann equation:developing more robust and efficient methods
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[Provides a description of an efficient multigrid algorithm for solving the PBE on a Cartesian mesh and reviews several methods for solution of nonlinear partial differential equations.]
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Holst MJ, Saied F (1995): Numerical solution of the nonlinear Poisson-Boltzmann equation:developing more robust and efficient methods. J Comput Chem 16:337-64. [Provides a description of an efficient multigrid algorithm for solving the PBE on a Cartesian mesh and reviews several methods for solution of nonlinear partial differential equations.]
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J Comput Chem
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Holst, M.J.1
Saied, F.2
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0032096837
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Continuum solvation models: computation of electrostatic forces from numerical solutions to the Poisson-Boltzmann equation
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[Introduces alternative definitions for the dielectric and ionic accessibility coefficients in the PBE and describes the calculation of electrostatic forces.]
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Im W, Beglov D, Roux B (1998): Continuum solvation models: computation of electrostatic forces from numerical solutions to the Poisson-Boltzmann equation. Comput Phys Chem 111:59-75. [Introduces alternative definitions for the dielectric and ionic accessibility coefficients in the PBE and describes the calculation of electrostatic forces.]
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Comput Phys Chem
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Im, W.1
Beglov, D.2
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0022964504
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Focusing of electric fields of the active site of Cu-Zn superoxide dismutase: effects of ionic strength and amino-acid modification
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[Introduced the finite-difference method for solving the linearized PBE for a protein with a realistic surface topography.]
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Klapper I, Hagstrom R, Fine R, Sharp K, Honig B (1986): Focusing of electric fields of the active site of Cu-Zn superoxide dismutase: effects of ionic strength and amino-acid modification. Proteins Struct Func Genet 1:47-59. [Introduced the finite-difference method for solving the linearized PBE for a protein with a realistic surface topography.]
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Proteins Struct Func Genet
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Klapper, I.1
Hagstrom, R.2
Fine, R.3
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[Describes protein titration in terms of a simple spherical model.]
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Electrostatic control of the membrane targeting of C2 domains. Molec Cell (Forthcoming) Poisson-Boltzmann electrostatics are used to predict the binding properties of C2 domains from a variety of proteins
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Murray D, Honig B (2002): Electrostatic control of the membrane targeting of C2 domains. Molec Cell (Forthcoming) Poisson-Boltzmann electrostatics are used to predict the binding properties of C2 domains from a variety of proteins. Molec Cell 9:145-54.
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Molec Cell
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Beyond Poisson-Boltzmann: fluctuation effects and correlation functions
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[Field theory derivation of the PBE and higher-order electrostatics formulations.]
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Eur Phys J
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Netz, R.R.1
Orland, H.2
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Brownian dynamics of diffusion-influenced bimolecular reactions
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[Presents the basic method for analyzing Brownian dynamics trajectories to calculate the rate constants of diffusional encounter of biopolymers or other molecules.]
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Northrup SH, Allison SA, McCammon JA (1984): Brownian dynamics of diffusion-influenced bimolecular reactions. J Chem Phys 80:1517-24. [Presents the basic method for analyzing Brownian dynamics trajectories to calculate the rate constants of diffusional encounter of biopolymers or other molecules.]
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J Chem Phys
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Northrup, S.H.1
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McCammon, J.A.3
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0034896467
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Thermodynamics and kinetics of actin filament nucleation
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[Poisson-Boltzmann and Brownian dynamics calculations are used to analyze the initial steps in the formation of actin filaments.]
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Sept D, McCammon JA (2001): Thermodynamics and kinetics of actin filament nucleation. Biophys J 81:667-74. [Poisson-Boltzmann and Brownian dynamics calculations are used to analyze the initial steps in the formation of actin filaments.]
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Biophys J
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McCammon, J.A.2
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Calculating total electrostatic energies with the nonlinear Poisson-Boltzmann equation
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Sharp KA, Honig B (1990): Calculating total electrostatic energies with the nonlinear Poisson-Boltzmann equation. J Phys Chem 94:7684-92. [Describes the calculation of electrostatic energies from the PBE.]
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J Phys Chem
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Semianalytical treatment of solvation for molecular mechanics and dynamics
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[Describes the development of the generalized Born method for biomolecular electrostatics.]
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Still, W.C.1
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33947468892
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Theory of protein titration curves. I. General equations for impenetrable spheres
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[Describes the electrostatics of a spherical protein with low dielectric coefficient and discrete, buried charges, immersed in a dilute electrolyte solution.]
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J Am Chem Soc
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Kirkwood, J.G.2
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0020475509
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Calculation of the electric potential in the active site cleft due to alpha-helix dipoles
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[First application of a finite-difference method to solve the Poisson equation for a protein with realistic surface topography.]
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Warwicker J, Watson HC (1982): Calculation of the electric potential in the active site cleft due to alpha-helix dipoles. J Mol Biol 157:671-9. [First application of a finite-difference method to solve the Poisson equation for a protein with realistic surface topography.]
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J Mol Biol
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Warwicker, J.1
Watson, H.C.2
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A new method for computing the macromolecular electric potential
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[Solution of the PBE by boundary element methods.]
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Zauhar R, Morgan RJ (1985): A new method for computing the macromolecular electric potential. J Mol Biol 186:815-20. [Solution of the PBE by boundary element methods.]
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J Mol Biol
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Zauhar, R.1
Morgan, R.J.2
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