Highly accurate biomolecular electrostatics in continuum dielectric environments
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[1] Soonmin Jang,et al. Molecular Dynamics Study of Peptides in Implicit Water: Ab Initio Folding of β-Hairpin, β-Sheet, and ββα-motif , 2002 .
[2] R. Zauhar,et al. A new method for computing the macromolecular electric potential. , 1985, Journal of molecular biology.
[3] David Andelman,et al. Electrostatic Properties of Membranes: The Poisson-Boltzmann Theory , 1995 .
[4] Michael Feig,et al. Molecular dynamics simulations of large integral membrane proteins with an implicit membrane model. , 2006, The journal of physical chemistry. B.
[5] Michael J. Holst,et al. Multigrid solution of the Poisson—Boltzmann equation , 1992, J. Comput. Chem..
[6] R. LeVeque,et al. A comparison of the extended finite element method with the immersed interface method for elliptic equations with discontinuous coefficients and singular sources , 2006 .
[7] Michael J. Holst,et al. Numerical solution of the nonlinear Poisson–Boltzmann equation: Developing more robust and efficient methods , 1995, J. Comput. Chem..
[8] B. Berne,et al. Can a continuum solvent model reproduce the free energy landscape of a β-hairpin folding in water? , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[9] B. Roux,et al. Implicit solvent models. , 1999, Biophysical chemistry.
[10] K. Sharp,et al. Electrostatic interactions in macromolecules: theory and applications. , 1990, Annual review of biophysics and biophysical chemistry.
[11] Ariel Fernández,et al. Continuum equations for dielectric response to macro-molecular assemblies at the nano scale , 2004 .
[12] Nathan A. Baker,et al. Electrostatics of nanosystems: Application to microtubules and the ribosome , 2001, Proceedings of the National Academy of Sciences of the United States of America.
[13] J. Israelachvili. Intermolecular and surface forces , 1985 .
[14] C. Brooks,et al. Recent advances in the development and application of implicit solvent models in biomolecule simulations. , 2004, Current opinion in structural biology.
[15] B. Honig,et al. Classical electrostatics in biology and chemistry. , 1995, Science.
[16] Ivo Babuska,et al. The finite element method for elliptic equations with discontinuous coefficients , 1970, Computing.
[17] Alexander D. MacKerell,et al. All-atom empirical potential for molecular modeling and dynamics studies of proteins. , 1998, The journal of physical chemistry. B.
[18] Eric J. Sorin,et al. β-hairpin folding simulations in atomistic detail using an implicit solvent model1 , 2001 .
[19] M. L. Connolly. Analytical molecular surface calculation , 1983 .
[20] W. Im,et al. Continuum solvation model: Computation of electrostatic forces from numerical solutions to the Poisson-Boltzmann equation , 1998 .
[21] 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 .
[22] M. Karplus,et al. CHARMM: A program for macromolecular energy, minimization, and dynamics calculations , 1983 .
[23] Douglas A. Lauffenburger,et al. NUMERICAL SOLUTION OF THE NONLINEAR POISSON-BOLTZMANN EQUATION FOR A MEMBRANE-ELECTROLYTE SYSTEM , 1994 .
[24] Shan Zhao,et al. High-order FDTD methods via derivative matching for Maxwell's equations with material interfaces , 2004 .
[25] C. Peskin. Numerical analysis of blood flow in the heart , 1977 .
[26] K. Sharp,et al. Calculating the electrostatic potential of molecules in solution: Method and error assessment , 1988 .
[27] V. Mikhailova,et al. Three-centered model of ultrafast photoinduced charge transfer: continuum dielectric approach. , 2006, The Journal of chemical physics.
[28] Nathan A. Baker,et al. Adaptive multilevel finite element solution of the Poisson–Boltzmann equation I. Algorithms and examples , 2000 .
[29] Ronald M. Levy,et al. AGBNP: An analytic implicit solvent model suitable for molecular dynamics simulations and high‐resolution modeling , 2004, J. Comput. Chem..
[30] Charles L. Brooks,et al. Performance comparison of generalized born and Poisson methods in the calculation of electrostatic solvation energies for protein structures , 2004, J. Comput. Chem..
[31] R. J. Hunter. Foundations of Colloid Science , 1987 .
[32] Richard A. Friesner,et al. Numerical solution of the Poisson–Boltzmann equation using tetrahedral finite‐element meshes , 1997 .
[33] Nathan A. Baker,et al. Improving implicit solvent simulations: a Poisson-centric view. , 2005, Current opinion in structural biology.
[34] Richard H. Henchman,et al. Revisiting free energy calculations: a theoretical connection to MM/PBSA and direct calculation of the association free energy. , 2004, Biophysical journal.
[35] Peijuan Zhu,et al. Implementation and testing of stable, fast implicit solvation in molecular dynamics using the smooth‐permittivity finite difference Poisson–Boltzmann method , 2004, J. Comput. Chem..
[36] Guo-Wei Wei,et al. On the fictitious-domain and interpolation formulations of the matched interface and boundary (MIB) method , 2006, J. Comput. Phys..
[37] Shan Zhao,et al. High order matched interface and boundary method for elliptic equations with discontinuous coefficients and singular sources , 2006, J. Comput. Phys..
[38] P. Kollman,et al. Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. , 2000, Accounts of chemical research.
[39] H. Scheraga,et al. A fast adaptive multigrid boundary element method for macromolecular electrostatic computations in a solvent , 1997 .
[40] J. Kirkwood,et al. Theory of Solutions of Molecules Containing Widely Separated Charges with Special Application to Zwitterions , 1934 .
[41] Donald Bashford,et al. Macroscopic electrostatic models for protonation states in proteins. , 2004, Frontiers in bioscience : a journal and virtual library.
[42] M. Sanner,et al. Reduced surface: an efficient way to compute molecular surfaces. , 1996, Biopolymers.
[43] Gerhard Hummer,et al. Simulation and Theory of Electrostatic Interactions in Solution: Computational Chemistry, Biophysics and Aqueous Solutions, Santa Fe, New Mexico, U. S. A., 23-25 June 1999 , 1999 .
[44] B. Honig,et al. Calculation of the total electrostatic energy of a macromolecular system: Solvation energies, binding energies, and conformational analysis , 1988, Proteins.
[45] P. Strevens. Iii , 1985 .
[46] S. Osher,et al. A Non-oscillatory Eulerian Approach to Interfaces in Multimaterial Flows (the Ghost Fluid Method) , 1999 .
[47] J. Andrew McCammon,et al. Solving the finite‐difference non‐linear Poisson–Boltzmann equation , 1992 .
[48] Federico Fogolari,et al. Protocol for MM/PBSA molecular dynamics simulations of proteins. , 2003, Biophysical journal.
[49] Ray Luo,et al. A Poisson–Boltzmann dynamics method with nonperiodic boundary condition , 2003 .