Ion counting from explicit-solvent simulations and 3D-RISM.
暂无分享,去创建一个
[1] D. Draper,et al. RNA folding: thermodynamic and molecular descriptions of the roles of ions. , 2008, Biophysical journal.
[2] Benoît Roux,et al. An Integral Equation To Describe the Solvation of Polar Molecules in Liquid Water , 1997 .
[3] Laxmikant V. Kalé,et al. Scalable molecular dynamics with NAMD , 2005, J. Comput. Chem..
[4] B. Montgomery Pettitt,et al. A site-site theory for finite concentration saline solutions , 1992 .
[5] M. Record,et al. Relative binding affinities of monovalent cations for double-stranded DNA. , 1980, Proceedings of the National Academy of Sciences of the United States of America.
[6] B. Brooks,et al. Constant pressure molecular dynamics simulation: The Langevin piston method , 1995 .
[7] T. Straatsma,et al. THE MISSING TERM IN EFFECTIVE PAIR POTENTIALS , 1987 .
[8] M. Klein,et al. Constant pressure molecular dynamics algorithms , 1994 .
[9] E. Ruckenstein,et al. A protein molecule in a mixed solvent: the preferential binding parameter via the Kirkwood-Buff theory. , 2006, Biophysical journal.
[10] M. Record,et al. Analysis of effects of salts and uncharged solutes on protein and nucleic acid equilibria and processes: a practical guide to recognizing and interpreting polyelectrolyte effects, Hofmeister effects, and osmotic effects of salts. , 1998, Advances in protein chemistry.
[11] D. Draper,et al. Ions and RNA folding. , 2005, Annual review of biophysics and biomolecular structure.
[12] Neocles B. Leontis,et al. Molecular modeling of nucleic acids , 1997 .
[13] Jens Kurreck,et al. Nucleic acids chemistry and biology. , 2003, Angewandte Chemie.
[14] Andriy Kovalenko,et al. Solution of three-dimensional reference interaction site model and hypernetted chain equations for simple point charge water by modified method of direct inversion in iterative subspace , 1999, J. Comput. Chem..
[15] T. Cheatham,et al. Determination of Alkali and Halide Monovalent Ion Parameters for Use in Explicitly Solvated Biomolecular Simulations , 2008, The journal of physical chemistry. B.
[16] Greg L. Hura,et al. Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew. , 2004, The Journal of chemical physics.
[17] Paul E. Smith,et al. Equilibrium dialysis data and the relationships between preferential interaction parameters for biological systems in terms of Kirkwood-Buff integrals. , 2006, The journal of physical chemistry. B.
[18] G. S. Manning. Electrostatic free energies of spheres, cylinders, and planes in counterion condensation theory with some applications , 2007 .
[19] C. Brooks. Computer simulation of liquids , 1989 .
[20] B. Honig,et al. Classical electrostatics in biology and chemistry. , 1995, Science.
[21] G. S. Manning. A counterion condensation theory for the relaxation, rise, and frequency dependence of the parallel polarization of rodlike polyelectrolytes , 2011, The European physical journal. E, Soft matter.
[22] D. N. Card,et al. Calculations on the ``Restricted Primitive Model'' for 1–1 Electrolyte Solutions , 1972 .
[23] Fumio Hirata,et al. Solution of three‐dimensional reference interaction site model and hypernetted chain equations for simple point charge water by modified method of direct inversion in iterative subspace , 1999 .
[24] Paul E. Smith,et al. Cosolvent Interactions with Biomolecules: Relating Computer Simulation Data to Experimental Thermodynamic Data , 2004 .
[25] David A. Case,et al. Modeling Unusual Nucleic Acid Structures , 1998 .
[26] D. Case,et al. Simple electrolyte solutions: comparison of DRISM and molecular dynamics results for alkali halide solutions. , 2013, The Journal of chemical physics.
[27] Otakar Sohnel,et al. Densities of aqueous solutions of inorganic substances , 1985 .
[28] W. L. Jorgensen,et al. Comparison of simple potential functions for simulating liquid water , 1983 .
[29] Nathan A. Baker,et al. Simulations of RNA interactions with monovalent ions. , 2009, Methods in enzymology.
[30] B. Luan,et al. DNA attraction in monovalent and divalent electrolytes. , 2008, Journal of the American Chemical Society.
[31] Carlos Simmerling,et al. Three-dimensional molecular theory of solvation coupled with molecular dynamics in Amber. , 2010, Journal of chemical theory and computation.
[32] M. Record,et al. Competitive interactions of Co(NH3)6(3+) and Na+ with helical B-DNA probed by 59Co and 23Na NMR. , 1987, Biochemistry.
[33] M. Record,et al. Ion distributions around DNA and other cylindrical polyions: theoretical descriptions and physical implications. , 1990, Annual review of biophysics and biophysical chemistry.
[34] M. Record,et al. Salt-nucleic acid interactions. , 1995, Annual review of physical chemistry.
[35] F. Hirata,et al. Application of the reference interaction site model theory to analysis on surface‐induced structure of water , 1996 .
[36] T. Darden,et al. Molecular dynamics simulations of biomolecules: long-range electrostatic effects. , 1999, Annual review of biophysics and biomolecular structure.
[37] Peter A. Kollman,et al. AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules , 1995 .
[38] R. Chitra,et al. Properties of 2,2,2-trifluoroethanol and water mixtures , 2001 .
[39] J. Naghizadeh. Counterion binding in polyelectrolyte theory , 1982 .
[40] Arieh Ben-Naim,et al. Statistical Thermodynamics for Chemists and Biochemists , 1992, Springer US.
[41] D W Hukins,et al. Optimised parameters for A-DNA and B-DNA. , 1972, Biochemical and biophysical research communications.
[42] F. J. Luque,et al. The impact of monovalent ion force field model in nucleic acids simulations. , 2009, Physical chemistry chemical physics : PCCP.
[43] Alexandre M.J.J. Bonvin,et al. Localisation and dynamics of sodium counterions around DNA in solution from molecular dynamics simulation , 2000, European Biophysics Journal.
[44] K. Ng. Hypernetted chain solutions for the classical one‐component plasma up to Γ=7000 , 1974 .
[45] D. Herschlag,et al. Probing nucleic acid-ion interactions with buffer exchange-atomic emission spectroscopy. , 2009, Methods in enzymology.
[46] 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.
[47] R. Pappu,et al. Molecular simulation studies of monovalent counterion-mediated interactions in a model RNA kissing loop. , 2009, Journal of molecular biology.
[48] Ron Elber,et al. RNA and its ionic cloud: solution scattering experiments and atomically detailed simulations. , 2012, Biophysical journal.
[49] Monika Eisenhower,et al. Molecular Theory Of Solutions , 2016 .
[50] F. Hirata,et al. Solvent and salt effects on structural stability of human telomere. , 2011, The journal of physical chemistry. B.
[51] G. S. Manning. The molecular theory of polyelectrolyte solutions with applications to the electrostatic properties of polynucleotides , 1978, Quarterly Reviews of Biophysics.
[52] J. Šponer,et al. Refinement of the AMBER Force Field for Nucleic Acids: Improving the Description of α/γ Conformers , 2007 .
[53] David Chandler,et al. Free energy functions in the extended RISM approximation , 1985 .
[54] I. R. Mcdonald,et al. Theory of simple liquids , 1998 .
[55] T. Darden,et al. A smooth particle mesh Ewald method , 1995 .
[56] H. Sigel,et al. Interplay between Metal Ions and Nucleic Acids , 2012 .
[57] M. Record,et al. Interpretation of preferential interaction coefficients of nonelectrolytes and of electrolyte ions in terms of a two-domain model. , 1995, Biophysical journal.
[58] D. Draper,et al. Mg2+–RNA interaction free energies and their relationship to the folding of RNA tertiary structures , 2006, Proceedings of the National Academy of Sciences.
[59] C. F. Anderson,et al. Competitive interactions of cobalt(3+)hexamine and sodium with helical B-DNA probed by cobalt-59 and sodium-23 NMR , 1987 .
[60] J. Springer,et al. Integral equation solutions for the classical electron gas , 1973 .
[61] E Westhof,et al. Water and ion binding around r(UpA)12 and d(TpA)12 oligomers--comparison with RNA and DNA (CpG)12 duplexes. , 2001, Journal of molecular biology.
[62] David E Draper,et al. Ion-RNA interactions thermodynamic analysis of the effects of mono- and divalent ions on RNA conformational equilibria. , 2009, Methods in enzymology.
[63] M. Record,et al. Polyelectrolyte Theories and their Applications to DNA , 1982 .
[64] Hans W. Horn,et al. Characterization of the TIP4P-Ew water model: vapor pressure and boiling point. , 2005, The Journal of chemical physics.
[65] B. Montgomery Pettitt,et al. Application of an extended RISM equation to dipolar and quadrupolar fluids , 1982 .
[66] B. Montgomery Pettitt,et al. A dielectrically consistent interaction site theory for solvent—electrolyte mixtures , 1992 .
[67] S. Lowen. The Biophysical Journal , 1960, Nature.
[68] T. Morita. Theory of Classical Fluids: Hyper-Netted Chain Approximation, I Formulation for a One-Component System , 1958 .
[69] Sebastian Doniach,et al. Evaluation of ion binding to DNA duplexes using a size-modified Poisson-Boltzmann theory. , 2007, Biophysical journal.
[70] Gillian C. Lynch,et al. Ion and solvent density distributions around canonical B-DNA from integral equations. , 2011, The journal of physical chemistry. B.
[71] R. Elber,et al. Computational exploration of mobile ion distributions around RNA duplex. , 2010, The journal of physical chemistry. B.
[72] Holger Gohlke,et al. The Amber biomolecular simulation programs , 2005, J. Comput. Chem..
[73] Fumio Hirata,et al. Molecular Theory of Solvation , 2004 .
[74] Charles A Laughton,et al. Exploring the counterion atmosphere around DNA: what can be learned from molecular dynamics simulations? , 2004, Biophysical journal.
[75] Ron Elber,et al. The ionic atmosphere around A-RNA: Poisson-Boltzmann and molecular dynamics simulations. , 2012, Biophysical journal.
[76] Andriy Kovalenko,et al. Efficient treatment of solvation shells in 3D molecular theory of solvation , 2012, J. Comput. Chem..
[77] Fumio Hirata,et al. Self-consistent description of a metal–water interface by the Kohn–Sham density functional theory and the three-dimensional reference interaction site model , 1999 .
[78] S. Kast,et al. Closed-form expressions of the chemical potential for integral equation closures with certain bridge functions. , 2008, The Journal of chemical physics.
[79] D. Herschlag,et al. Quantitative and comprehensive decomposition of the ion atmosphere around nucleic acids. , 2007, Journal of the American Chemical Society.
[80] Accidental deviations of density and opalescence at the critical point of a single substance , 2010 .
[81] Fumio Hirata,et al. Potentials of mean force of simple ions in ambient aqueous solution. I. Three-dimensional reference interaction site model approach , 2000 .
[82] Andriy Kovalenko,et al. Three-dimensional Rism Theory for Molecular Liquids and Solid-Liquid Interfaces , 2004 .
[83] G. Ciccotti,et al. Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes , 1977 .
[84] Norio Yoshida,et al. Revisiting the salt-induced conformational change of DNA with 3D-RISM theory. , 2010, The journal of physical chemistry. B.
[85] B. Montgomery Pettitt,et al. Integral equation predictions of liquid state structure for waterlike intermolecular potentials , 1982 .
[86] Jejoong Yoo,et al. Improved Parametrization of Li+, Na+, K+, and Mg2+ Ions for All-Atom Molecular Dynamics Simulations of Nucleic Acid Systems , 2012 .
[87] Junmei Wang,et al. How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? , 2000, J. Comput. Chem..
[88] Gillian C. Lynch,et al. Protein solvation from theory and simulation: Exact treatment of Coulomb interactions in three-dimensional theories. , 2010, The Journal of chemical physics.
[89] Michal Otyepka,et al. Performance of Molecular Mechanics Force Fields for RNA Simulations: Stability of UUCG and GNRA Hairpins. , 2010, Journal of chemical theory and computation.
[90] G. S. Manning,et al. Counterion condensation on charged spheres, cylinders, and planes. , 2007, The journal of physical chemistry. B.
[91] Christopher D. Jones,et al. Counting ions around DNA with anomalous small-angle X-ray scattering. , 2010, Journal of the American Chemical Society.
[92] L. Pollack,et al. Both helix topology and counterion distribution contribute to the more effective charge screening in dsRNA compared with dsDNA , 2009, Nucleic acids research.
[93] I. R. Mcdonald,et al. Statistical mechanics of dense ionized matter. IV. Density and charge fluctuations in a simple molten salt , 1975 .
[94] E Westhof,et al. Water and ion binding around RNA and DNA (C,G) oligomers. , 2000, Journal of molecular biology.
[95] M. Lozada-Cassou,et al. Hypernetted chain approximation for the distribution of ions around a cylindrical electrode. II. Numerical solution for a model cylindrical polyelectrolyte , 1985 .
[96] D. Beveridge,et al. Dynamics of water and ions near DNA: comparison of simulation to time-resolved stokes-shift experiments. , 2009, Journal of the American Chemical Society.
[97] Molecular dynamics simulation of multivalent-ion mediated attraction between DNA molecules. , 2008, Physical review letters.
[98] L. Pollack. SAXS studies of ion-nucleic acid interactions. , 2011, Annual review of biophysics.
[99] Kelly M. Thayer,et al. Ion motions in molecular dynamics simulations on DNA. , 2004, Proceedings of the National Academy of Sciences of the United States of America.
[100] Stephen Neidle,et al. Principles of nucleic acid structure , 2007 .
[101] A. Lyubartsev. Molecular Simulations of DNA Counterion Distributions , 2004 .
[102] J. Bond,et al. Conformational transitions of duplex and triplex nucleic acid helices: thermodynamic analysis of effects of salt concentration on stability using preferential interaction coefficients. , 1994, Biophysical journal.
[103] A. Lyubartsev,et al. A molecular dynamics simulation study of oriented DNA with polyamine and sodium counterions: diffusion and averaged binding of water and cations. , 2003, Nucleic acids research.
[104] Fumio Hirata,et al. An extended rism equation for molecular polar fluids , 1981 .
[105] M. Gillan,et al. A new method of solving the HNC equation for ionic liquids , 1980 .
[106] F. Millero. The apparent and partial molal volume of aqueous sodium chloride solutions at various temperatures , 1970 .
[107] Thomas Simonson,et al. Electrostatics and dynamics of proteins , 2003 .