Electrostatic forces in the Poisson-Boltzmann systems.
暂无分享,去创建一个
Ray Luo | Qin Cai | Jun Wang | R. Luo | Qin Cai | Li Xiao | Jun Wang | Li Xiao | Xiang Ye | Xiang Ye
[1] H. Scheraga,et al. A fast adaptive multigrid boundary element method for macromolecular electrostatic computations in a solvent , 1997 .
[2] A. Rashin. Electrostatics of ion-ion interactions in solution , 1989 .
[3] Ruhong Zhou,et al. Poisson−Boltzmann Analytical Gradients for Molecular Modeling Calculations , 1999 .
[4] H. Zhou,et al. Boundary element solution of macromolecular electrostatics: interaction energy between two proteins. , 1993, Biophysical journal.
[5] Klaus Schulten,et al. Molecular Dynamics Simulations in Heterogeneous Dielectrica and Debye-Hückel Media - Application to the Protein Bovine Pancreatic Trypsin Inhibitor , 1992 .
[6] B. Honig,et al. A rapid finite difference algorithm, utilizing successive over‐relaxation to solve the Poisson–Boltzmann equation , 1991 .
[7] Nathan A. Baker,et al. Adaptive multilevel finite element solution of the Poisson–Boltzmann equation I. Algorithms and examples , 2000 .
[8] K. Sharp,et al. Macroscopic models of aqueous solutions : biological and chemical applications , 1993 .
[9] Nathan A. Baker,et al. Improving implicit solvent simulations: a Poisson-centric view. , 2005, Current opinion in structural biology.
[10] Michael J. Holst,et al. Numerical solution of the nonlinear Poisson–Boltzmann equation: Developing more robust and efficient methods , 1995, J. Comput. Chem..
[11] M. Karplus,et al. pKa's of ionizable groups in proteins: atomic detail from a continuum electrostatic model. , 1990, Biochemistry.
[12] Y. C. Zhou,et al. Poisson-Nernst-Planck equations for simulating biomolecular diffusion-reaction processes II: size effects on ionic distributions and diffusion-reaction rates. , 2011, Biophysical journal.
[13] Richard A. Friesner,et al. Numerical solution of the Poisson–Boltzmann equation using tetrahedral finite‐element meshes , 1997 .
[14] R. Zauhar,et al. The incorporation of hydration forces determined by continuum electrostatics into molecular mechanics simulations , 1991 .
[15] Benzhuo Lu,et al. Improved Boundary Element Methods for Poisson-Boltzmann Electrostatic Potential and Force Calculations. , 2007, Journal of chemical theory and computation.
[16] Bo Li,et al. Dielectric Boundary Force in Molecular Solvation with the Poisson-Boltzmann Free Energy: A Shape Derivative Approach , 2011, SIAM J. Appl. Math..
[17] Barry Honig,et al. Extending the Applicability of the Nonlinear Poisson−Boltzmann Equation: Multiple Dielectric Constants and Multivalent Ions† , 2001 .
[18] Barry Honig,et al. Focusing of electric fields in the active site of Cu‐Zn superoxide dismutase: Effects of ionic strength and amino‐acid modification , 1986, Proteins.
[19] Evgenii Mikhailovich Lifshitz,et al. ELECTROSTATICS OF CONDUCTORS , 1984 .
[20] D. Case,et al. Generalized born models of macromolecular solvation effects. , 2000, Annual review of physical chemistry.
[21] H. Berendsen,et al. The electric potential of a macromolecule in a solvent: A fundamental approach , 1991 .
[22] Ray Luo,et al. Dielectric Boundary Forces in Numerical Poisson-Boltzmann Methods: Theory and Numerical Strategies. , 2011, Chemical physics letters.
[23] Anna Tempczyk,et al. Electrostatic contributions to solvation energies: comparison of free energy perturbation and continuum calculations , 1991 .
[24] J. Milovich,et al. Solution of the nonlinear Poisson-Boltzmann equation using pseudo-transient continuation and the finite element method. , 2002, Journal of colloid and interface science.
[25] Barry Honig,et al. Calculating total electrostatic energies with the nonlinear Poisson-Boltzmann equation , 1990 .
[26] B. J. Yoon,et al. A boundary element method for molecular electrostatics with electrolyte effects , 1990 .
[27] R. Luo,et al. Reducing grid-dependence in finite-difference Poisson-Boltzmann calculations. , 2012, Journal of chemical theory and computation.
[28] Ray Luo,et al. Performance of Nonlinear Finite-Difference Poisson-Boltzmann Solvers. , 2010, Journal of chemical theory and computation.
[29] Enrico O. Purisima,et al. A simple yet accurate boundary element method for continuum dielectric calculations , 1995, J. Comput. Chem..
[30] Donald Bashford,et al. An Object-Oriented Programming Suite for Electrostatic Effects in Biological Molecules , 1997, ISCOPE.
[31] Dexuan Xie,et al. A new minimization protocol for solving nonlinear Poisson–Boltzmann mortar finite element equation , 2007 .
[32] Marcia O. Fenley,et al. Fast Boundary Element Method for the Linear Poisson-Boltzmann Equation , 2002 .
[33] Ray Luo,et al. Assessment of linear finite‐difference Poisson–Boltzmann solvers , 2010, J. Comput. Chem..
[34] Benzhuo Lu,et al. Computation of electrostatic forces between solvated molecules determined by the Poisson-Boltzmann equation using a boundary element method. , 2005, The Journal of chemical physics.
[35] Ray Luo,et al. Accelerated Poisson–Boltzmann calculations for static and dynamic systems , 2002, J. Comput. Chem..
[36] R. Zauhar,et al. The rigorous computation of the molecular electric potential , 1988 .
[37] S Subramaniam,et al. Computation of molecular electrostatics with boundary element methods. , 1997, Biophysical journal.
[38] Kim A. Sharp,et al. Incorporating solvent and ion screening into molecular dynamics using the finite‐difference Poisson–Boltzmann method , 1991 .
[39] K. Sharp,et al. Electrostatic interactions in macromolecules: theory and applications. , 1990, Annual review of biophysics and biophysical chemistry.
[40] B. Honig,et al. Classical electrostatics in biology and chemistry. , 1995, Science.
[41] J. Warwicker,et al. Calculation of the electric potential in the active site cleft due to alpha-helix dipoles. , 1982, Journal of molecular biology.
[42] Nathan A. Baker,et al. Adaptive multilevel finite element solution of the Poisson–Boltzmann equation II. Refinement at solvent‐accessible surfaces in biomolecular systems , 2000 .
[43] Michael Feig,et al. Extending the horizon: towards the efficient modeling of large biomolecular complexes in atomic detail , 2006 .
[44] C. Cramer,et al. Implicit Solvation Models: Equilibria, Structure, Spectra, and Dynamics. , 1999, Chemical reviews.
[45] R Abagyan,et al. Rapid boundary element solvation electrostatics calculations in folding simulations: successful folding of a 23-residue peptide. , 2001, Biopolymers.
[46] J. Andrew McCammon,et al. Electrostatic energy calculations by a Finite‐difference method: Rapid calculation of charge–solvent interaction energies , 1992 .
[47] James Andrew McCammon,et al. Molecular dynamics simulation with a continuum electrostatic model of the solvent , 1995, J. Comput. Chem..
[48] J. A. McCammon,et al. Calculating electrostatic forces from grid‐calculated potentials , 1990 .
[49] Jacob K. White,et al. Accurate solution of multi‐region continuum biomolecule electrostatic problems using the linearized Poisson–Boltzmann equation with curved boundary elements , 2009, J. Comput. Chem..
[50] S. Sriharan,et al. The fast multipole boundary element method for molecular electrostatics: An optimal approach for large systems , 1995, J. Comput. Chem..
[51] Ray Luo,et al. Dielectric pressure in continuum electrostatic solvation of biomolecules. , 2012, Physical chemistry chemical physics : PCCP.
[52] Eric C. Cyr,et al. A first‐order system least‐squares finite element method for the Poisson‐Boltzmann equation , 2009, J. Comput. Chem..
[53] M K Gilson,et al. Theory of electrostatic interactions in macromolecules. , 1995, Current opinion in structural biology.
[54] Benzhuo Lu,et al. Order N algorithm for computation of electrostatic interactions in biomolecular systems , 2006, Proceedings of the National Academy of Sciences.
[55] J. Andrew McCammon,et al. Solving the finite‐difference non‐linear Poisson–Boltzmann equation , 1992 .
[56] Chandrajit L. Bajaj,et al. An Efficient Higher-Order Fast Multipole Boundary Element Solution for Poisson-Boltzmann-Based Molecular Electrostatics , 2011, SIAM J. Sci. Comput..
[57] C. Brooks,et al. Balancing solvation and intramolecular interactions: toward a consistent generalized Born force field. , 2006, Journal of the American Chemical Society.
[58] P. Koehl. Electrostatics calculations: latest methodological advances. , 2006, Current opinion in structural biology.
[59] C. Brooks,et al. Peptide and protein folding and conformational equilibria: theoretical treatment of electrostatics and hydrogen bonding with implicit solvent models. , 2005, Advances in protein chemistry.
[60] Benzhuo Lu,et al. An Adaptive Fast Multipole Boundary Element Method for Poisson−Boltzmann Electrostatics , 2009, Journal of chemical theory and computation.
[61] Ray Luo,et al. Chapter Six - Poisson–Boltzmann Implicit Solvation Models , 2012 .
[62] Malcolm E. Davis,et al. Electrostatics in biomolecular structure and dynamics , 1990 .
[63] Alexander A. Rashin,et al. Hydration phenomena, classical electrostatics, and the boundary element method , 1990 .
[64] R. Zauhar,et al. A new method for computing the macromolecular electric potential. , 1985, Journal of molecular biology.
[65] J Andrew McCammon,et al. Electrostatic Free Energy and Its Variations in Implicit Solvent Models , 2022 .
[66] Robert E. Bruccoleri,et al. Grid positioning independence and the reduction of self‐energy in the solution of the Poisson—Boltzmann equation , 1993, J. Comput. Chem..
[67] Benoît Roux,et al. Solvation of complex molecules in a polar liquid: An integral equation theory , 1996 .
[68] J. Andrew McCammon,et al. Computation of electrostatic forces on solvated molecules using the Poisson-Boltzmann equation , 1993 .
[69] J. Tomasi,et al. Electrostatic interaction of a solute with a continuum. A direct utilizaion of AB initio molecular potentials for the prevision of solvent effects , 1981 .
[70] Michael J. Holst,et al. Multigrid solution of the Poisson—Boltzmann equation , 1992, J. Comput. Chem..
[71] W. Im,et al. Continuum solvation model: Computation of electrostatic forces from numerical solutions to the Poisson-Boltzmann equation , 1998 .
[72] Douglas A. Lauffenburger,et al. NUMERICAL SOLUTION OF THE NONLINEAR POISSON-BOLTZMANN EQUATION FOR A MEMBRANE-ELECTROLYTE SYSTEM , 1994 .
[73] J. Andrew McCammon,et al. Dielectric boundary smoothing in finite difference solutions of the poisson equation: An approach to improve accuracy and convergence , 1991 .
[74] Minoru Sakurai,et al. Medium effects on the molecular electronic structure. I. The formulation of a theory for the estimation of a molecular electronic structure surrounded by an anisotropic medium , 1987 .
[75] Harold A. Scheraga,et al. A combined iterative and boundary-element approach for solution of the nonlinear Poisson-Boltzmann equation , 1992 .
[76] Michael J. Holst,et al. Poisson-Nernst-Planck equations for simulating biomolecular diffusion-reaction processes I: Finite element solutions , 2010, J. Comput. Phys..
[77] Holger Gohlke,et al. The Amber biomolecular simulation programs , 2005, J. Comput. Chem..
[78] J. A. McCammon,et al. Solving the finite difference linearized Poisson‐Boltzmann equation: A comparison of relaxation and conjugate gradient methods , 1989 .
[79] Richard A. Friesner,et al. An automatic three‐dimensional finite element mesh generation system for the Poisson–Boltzmann equation , 1997 .
[80] Richard A. Friesner,et al. Solvation Free Energies of Peptides: Comparison of Approximate Continuum Solvation Models with Accurate Solution of the Poisson−Boltzmann Equation , 1997 .
[81] B. J. Yoon,et al. Computation of the electrostatic interaction energy between a protein and a charged surface , 1992 .
[82] J. Andrew Grant,et al. A smooth permittivity function for Poisson–Boltzmann solvation methods , 2001, J. Comput. Chem..
[83] Michael J. Holst,et al. The Finite Element Approximation of the Nonlinear Poisson-Boltzmann Equation , 2007, SIAM J. Numer. Anal..