메뉴 건너뛰기




Volumn , Issue , 2005, Pages 427-440

Electrostatic Interactions

Author keywords

Cartesian measures; Electrostatic interactions; Poisson Boltzman solver technology

Indexed keywords

COULOMB INTERACTIONS;

EID: 85050271404     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/0471721204.ch21     Document Type: Chapter
Times cited : (2)

References (27)
  • 1
  • 2
    • 0003966593 scopus 로고    scopus 로고
    • New York: Cambridge University Press. [Provides descriptions of finite difference and finite element methods as well as several solution methods for partial differential equations.]
    • 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.]
    • (1997) Finite Elements. Theory, Fast Solvers, and Applications in Solid Mechanics
    • Braess, D.1
  • 3
    • 85080416396 scopus 로고    scopus 로고
    • Introduction to continuum electrostatics, with molecular applications
    • In:Beard DA, editor., Biophysics textbook online at, [Review of continuum electrostatics concepts and methods.]
    • Gilson M (2002): Introduction to continuum electrostatics, with molecular applications. In:Beard DA, editor. Computational and Theoretical Biophysics. Biophysics textbook online at http://www.biophysics.org/btol/compute.html#3C. [Review of continuum electrostatics concepts and methods.]
    • (2002) Computational and Theoretical Biophysics
    • Gilson, M.1
  • 4
    • 0041993435 scopus 로고
    • New York: John Wiley & Sons. [Standard reference text for continuum electrostatics.]
    • Jackson JD (1975): Classical Electrostatics. New York: John Wiley & Sons. [Standard reference text for continuum electrostatics.]
    • (1975) Classical Electrostatics
    • Jackson, J.D.1
  • 5
    • 0000486194 scopus 로고    scopus 로고
    • Adaptive multilevel finite element solution of the Poisson-Boltzmann equation II: refinement at solvent accessible surfaces in biomolecular systems
    • [This article describes the application of finite element methods to the solution of the PBE.]
    • 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.]
    • (2000) J Comput Chem , vol.21 , pp. 1343-1352
    • Baker, N.A.1    Holst, M.J.2    Wang, F.3
  • 6
    • 0035964342 scopus 로고    scopus 로고
    • Electrostatics of cellular components: application to microtubules and the ribosome
    • USA, [This article describes the efficient parallel solution of the Poisson-Boltzmann equation for large biomolecules.]
    • 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.]
    • (2001) Proc Natl Acad Sci , vol.89 , pp. 10037-10041
    • Baker, N.A.1    Sept, D.2    Joseph, S.3    Holst, M.J.4    McCammon, J.A.5
  • 7
    • 0035327566 scopus 로고    scopus 로고
    • The adaptive multilevel finite element solution of the Poisson-Boltzmann equation on massively parallel computers
    • [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.]
    • 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.]
    • (2001) IBM J Res Dev , vol.45 , pp. 427-438
    • Baker, N.A.1    Sept, D.2    Holst, M.J.3    McCammon, J.A.4
  • 8
    • 34250928962 scopus 로고
    • Volumen und hydratationswärme der ionen
    • [Introduced an electrostatic model for ion solvation.]
    • Born M (1920): Volumen und hydratationswärme der ionen. Z Phys 1:45-8. [Introduced an electrostatic model for ion solvation.]
    • (1920) Z Phys , vol.1 , pp. 45-48
    • Born, M.1
  • 9
    • 0035281357 scopus 로고    scopus 로고
    • Computer simulation of protein-protein interactions
    • [A review of modern methods for simulating interactions between proteins.]
    • 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.]
    • (2001) J Phys Chem B , vol.105 , pp. 1504-1518
    • Elcock, A.H.1    Sept, D.2    McCammon, J.A.3
  • 10
    • 33750652614 scopus 로고
    • Brownian dynamics with hydrodynamic interactions
    • [Introduced the method for simulating the diffusional motion of biopolymers or other molecules, including the effects of electrostatic interactions.]
    • 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.]
    • (1978) J Chem Phys , vol.69 , pp. 1352-1360
    • Ermak, D.L.1    McCammon, J.A.2
  • 11
    • 0019808548 scopus 로고
    • Electrostatic contributions to the energetics of dimer-tetramer assembly in human hemoglobin: pH dependence and effect of specifically bound chloride ions
    • [Uses the Tanford-Kirkwood model for protein titration to determine pH effects on hemoglobin dimer-tetramer assembly.]
    • 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.]
    • (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
  • 12
    • 0035830963 scopus 로고    scopus 로고
    • Protein-protein association: investigation of factors influencing association rates by Brownian dynamics simulations
    • [Provides an analysis of the diffusional encounter simulations of a variety of different pairs of proteins.]
    • 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.]
    • (2001) J Mol Biol , vol.306 , pp. 1139-1155
    • Gabdoulline, R.R.1    Wade, R.C.2
  • 13
    • 0001585447 scopus 로고
    • Computation of electrostatic forces on solvated molecules using the Poisson-Boltzmann equation
    • [Description of the calculation of forces from solutions to PBE.]
    • 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.]
    • (1993) J Phys Chem , vol.97 , pp. 3591-3600
    • Gilson, M.K.1    Davis, M.E.2    Luty, B.3    McCammon, J.A.4
  • 14
    • 0000486193 scopus 로고    scopus 로고
    • Adaptive multilevel finite element solution of the Poisson-Boltzmann equation I: algorithms and examples
    • 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.
    • (2000) J Comput Chem , vol.21 , pp. 1319-1342
    • Holst, M.J.1    Baker, N.A.2    Wang, F.3
  • 15
    • 84986437211 scopus 로고
    • Numerical solution of the nonlinear Poisson-Boltzmann equation:developing more robust and efficient methods
    • [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.]
    • 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.]
    • (1995) J Comput Chem , vol.16 , pp. 337-364
    • Holst, M.J.1    Saied, F.2
  • 16
    • 0032096837 scopus 로고    scopus 로고
    • Continuum solvation models: computation of electrostatic forces from numerical solutions to the Poisson-Boltzmann equation
    • [Introduces alternative definitions for the dielectric and ionic accessibility coefficients in the PBE and describes the calculation of electrostatic forces.]
    • 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.]
    • (1998) Comput Phys Chem , vol.111 , pp. 59-75
    • Im, W.1    Beglov, D.2    Roux, B.3
  • 17
    • 0022964504 scopus 로고
    • Focusing of electric fields of the active site of Cu-Zn superoxide dismutase: effects of ionic strength and amino-acid modification
    • [Introduced the finite-difference method for solving the linearized PBE for a protein with a realistic surface topography.]
    • 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.]
    • (1986) Proteins Struct Func Genet , vol.1 , pp. 47-59
    • Klapper, I.1    Hagstrom, R.2    Fine, R.3    Sharp, K.4    Honig, B.5
  • 18
    • 85080406236 scopus 로고
    • [Describes protein titration in terms of a simple spherical model.]
    • Linderstrom-Lang K (1924): C. R. Travl. Lab. Carlsberg 15(7): [Describes protein titration in terms of a simple spherical model.]
    • (1924) C. R. Travl. Lab. Carlsberg , vol.15 , Issue.7
    • Linderstrom-Lang, K.1
  • 19
    • 0036161583 scopus 로고    scopus 로고
    • 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
    • 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.
    • (2002) Molec Cell , vol.9 , pp. 145-154
    • Murray, D.1    Honig, B.2
  • 20
    • 0001020827 scopus 로고    scopus 로고
    • Beyond Poisson-Boltzmann: fluctuation effects and correlation functions
    • [Field theory derivation of the PBE and higher-order electrostatics formulations.]
    • Netz RR, Orland H (2000): Beyond Poisson-Boltzmann: fluctuation effects and correlation functions. Eur Phys J 1:203-14. [Field theory derivation of the PBE and higher-order electrostatics formulations.]
    • (2000) Eur Phys J , vol.1 , pp. 203-214
    • Netz, R.R.1    Orland, H.2
  • 21
    • 36549102274 scopus 로고
    • Brownian dynamics of diffusion-influenced bimolecular reactions
    • [Presents the basic method for analyzing Brownian dynamics trajectories to calculate the rate constants of diffusional encounter of biopolymers or other molecules.]
    • 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.]
    • (1984) J Chem Phys , vol.80 , pp. 1517-1524
    • Northrup, S.H.1    Allison, S.A.2    McCammon, J.A.3
  • 22
    • 0034896467 scopus 로고    scopus 로고
    • Thermodynamics and kinetics of actin filament nucleation
    • [Poisson-Boltzmann and Brownian dynamics calculations are used to analyze the initial steps in the formation of actin filaments.]
    • 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.]
    • (2001) Biophys J , vol.81 , pp. 667-674
    • Sept, D.1    McCammon, J.A.2
  • 23
    • 33751552991 scopus 로고
    • Calculating total electrostatic energies with the nonlinear Poisson-Boltzmann equation
    • [Describes the calculation of electrostatic energies from the PBE.]
    • 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.]
    • (1990) J Phys Chem , vol.94 , pp. 7684-7692
    • Sharp, K.A.1    Honig, B.2
  • 24
    • 0344778061 scopus 로고
    • Semianalytical treatment of solvation for molecular mechanics and dynamics
    • [Describes the development of the generalized Born method for biomolecular electrostatics.]
    • Still WC, Tempczyk A, Hawley RC, Hendrickson T (1990): Semianalytical treatment of solvation for molecular mechanics and dynamics. J Am Chem Soc 112:6127-9. [Describes the development of the generalized Born method for biomolecular electrostatics.]
    • (1990) J Am Chem Soc , vol.112 , pp. 6127-6129
    • Still, W.C.1    Tempczyk, A.2    Hawley, R.C.3    Hendrickson, T.4
  • 25
    • 33947468892 scopus 로고
    • Theory of protein titration curves. I. General equations for impenetrable spheres
    • [Describes the electrostatics of a spherical protein with low dielectric coefficient and discrete, buried charges, immersed in a dilute electrolyte solution.]
    • Tanford C, Kirkwood JG (1957): Theory of protein titration curves. I. General equations for impenetrable spheres. J Am Chem Soc 79:5333-9. [Describes the electrostatics of a spherical protein with low dielectric coefficient and discrete, buried charges, immersed in a dilute electrolyte solution.]
    • (1957) J Am Chem Soc , vol.79 , pp. 5333-5339
    • Tanford, C.1    Kirkwood, J.G.2
  • 26
    • 0020475509 scopus 로고
    • Calculation of the electric potential in the active site cleft due to alpha-helix dipoles
    • [First application of a finite-difference method to solve the Poisson equation for a protein with realistic surface topography.]
    • 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.]
    • (1982) J Mol Biol , vol.157 , pp. 671-679
    • Warwicker, J.1    Watson, H.C.2
  • 27
    • 0022429751 scopus 로고
    • A new method for computing the macromolecular electric potential
    • [Solution of the PBE by boundary element methods.]
    • 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.]
    • (1985) J Mol Biol , vol.186 , pp. 815-820
    • Zauhar, R.1    Morgan, R.J.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.