The electrostatic response of water to neutral polar solutes: implications for continuum solvent modeling.
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Andrew T. Fenley | Michael K Gilson | Neil V Sapra | Andrew T Fenley | M. Gilson | H. Muddana | N. Sapra | Hari S Muddana
[1] Jindřich Fanfrlík,et al. Semiempirical Quantum Chemical PM6 Method Augmented by Dispersion and H-Bonding Correction Terms Reliably Describes Various Types of Noncovalent Complexes. , 2009, Journal of chemical theory and computation.
[2] Michael K. Gilson,et al. Blind prediction of host–guest binding affinities: a new SAMPL3 challenge , 2012, Journal of Computer-Aided Molecular Design.
[3] Steven W. Rick,et al. The Aqueous Solvation of Water: A Comparison of Continuum Methods with Molecular Dynamics , 1994 .
[4] Ray Luo,et al. Accelerated Poisson–Boltzmann calculations for static and dynamic systems , 2002, J. Comput. Chem..
[5] Zhan Chen,et al. Differential geometry based solvation model II: Lagrangian formulation , 2011, Journal of mathematical biology.
[6] Martin Korth,et al. Third-Generation Hydrogen-Bonding Corrections for Semiempirical QM Methods and Force Fields , 2010 .
[7] R. Friesner,et al. Generalized Born Model Based on a Surface Integral Formulation , 1998 .
[8] K. Sharp,et al. Electrostatic interactions in macromolecules: theory and applications. , 1990, Annual review of biophysics and biophysical chemistry.
[9] Ronald M. Levy,et al. Gaussian fluctuation formula for electrostatic free‐energy changes in solution , 1991 .
[10] H. Berendsen,et al. Molecular dynamics with coupling to an external bath , 1984 .
[11] David L Mobley,et al. Small molecule hydration free energies in explicit solvent: An extensive test of fixed-charge atomistic simulations. , 2009, Journal of chemical theory and computation.
[12] M. Shirts,et al. The solvation interface is a determining factor in peptide conformational preferences. , 2006, Journal of molecular biology.
[13] Charles H. Bennett,et al. Efficient estimation of free energy differences from Monte Carlo data , 1976 .
[14] W. L. Jorgensen,et al. Comparison of simple potential functions for simulating liquid water , 1983 .
[15] Richard A. Friesner,et al. Integrated Modeling Program, Applied Chemical Theory (IMPACT) , 2005, J. Comput. Chem..
[16] T. Straatsma,et al. Multiconfiguration thermodynamic integration , 1991 .
[17] Ken A Dill,et al. Ion pairing in molecular simulations of aqueous alkali halide solutions. , 2009, The journal of physical chemistry. B.
[18] S. Gavryushov. Electrostatics of B-DNA in NaCl and CaCl2 solutions: ion size, interionic correlation, and solvent dielectric saturation effects. , 2008, The journal of physical chemistry. B.
[19] T. Darden,et al. A smooth particle mesh Ewald method , 1995 .
[20] Yanli Wang,et al. PubChem: a public information system for analyzing bioactivities of small molecules , 2009, Nucleic Acids Res..
[21] I. Danielewicz-Ferchmin,et al. Static permittivity of water revisited: ε in the electric field above 108 V m−1 and in the temperature range 273≤T≤373 K , 2004 .
[22] P. Kollman,et al. A well-behaved electrostatic potential-based method using charge restraints for deriving atomic char , 1993 .
[23] Stephen L Mayo,et al. Electrostatics in computational protein design. , 2005, Current opinion in chemical biology.
[24] J. Ladbury. Just add water! The effect of water on the specificity of protein-ligand binding sites and its potential application to drug design. , 1996, Chemistry & biology.
[25] Andrew T. Fenley,et al. Analytical electrostatics for biomolecules: beyond the generalized Born approximation. , 2006, The Journal of chemical physics.
[26] W. C. Still,et al. Semianalytical treatment of solvation for molecular mechanics and dynamics , 1990 .
[27] F M Richards,et al. Areas, volumes, packing and protein structure. , 1977, Annual review of biophysics and bioengineering.
[28] Ronald M. Levy,et al. AGBNP: An analytic implicit solvent model suitable for molecular dynamics simulations and high‐resolution modeling , 2004, J. Comput. Chem..
[29] Carsten Kutzner,et al. GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation. , 2008, Journal of chemical theory and computation.
[30] Nathan A. Baker,et al. Biomolecular electrostatics and solvation: a computational perspective , 2012, Quarterly Reviews of Biophysics.
[31] Y. Marcus. Electrostriction in electrolyte solutions. , 2011, Chemical reviews.
[32] James J. P. Stewart,et al. MOPAC: A semiempirical molecular orbital program , 1990, J. Comput. Aided Mol. Des..
[33] Bhyravabhotla Jayaram,et al. Free energy calculations of ion hydration: an analysis of the Born model in terms of microscopic simulations , 1989 .
[34] T. Hansson,et al. On the Validity of Electrostatic Linear Response in Polar Solvents , 1996 .
[35] F. Allen. The Cambridge Structural Database: a quarter of a million crystal structures and rising. , 2002, Acta crystallographica. Section B, Structural science.
[36] Michael K. Gilson,et al. A synthetic host-guest system achieves avidin-biotin affinity by overcoming enthalpy–entropy compensation , 2007, Proceedings of the National Academy of Sciences.
[37] E. Whalley. Some Comments on Electrostatic Volumes and Entropies of Solvation , 1963 .
[38] R. Levy,et al. Field strength dependence of dielectric saturation in liquid water , 1990 .
[39] M. Gilson,et al. Calculation of Host-Guest Binding Affinities Using a Quantum-Mechanical Energy Model. , 2012, Journal of chemical theory and computation.
[40] Nathan A. Baker,et al. Differential geometry based solvation model I: Eulerian formulation , 2010, J. Comput. Phys..
[41] D. Case,et al. Modification of the Generalized Born Model Suitable for Macromolecules , 2000 .
[42] Michael Feig,et al. Extending the horizon: towards the efficient modeling of large biomolecular complexes in atomic detail , 2006 .
[43] D. Case,et al. Generalized born models of macromolecular solvation effects. , 2000, Annual review of physical chemistry.
[44] T. Ichiye,et al. Nonlinear response in ionic solvation: A theoretical investigation , 1998 .
[45] K. Sharp,et al. Finite difference Poisson‐Boltzmann electrostatic calculations: Increased accuracy achieved by harmonic dielectric smoothing and charge antialiasing , 1997 .
[46] J. Onuchic,et al. Water mediation in protein folding and molecular recognition. , 2006, Annual review of biophysics and biomolecular structure.
[47] Michael K Gilson,et al. New ultrahigh affinity host-guest complexes of cucurbit[7]uril with bicyclo[2.2.2]octane and adamantane guests: thermodynamic analysis and evaluation of M2 affinity calculations. , 2011, Journal of the American Chemical Society.
[48] Piotr Cieplak,et al. The R.E.D. tools: advances in RESP and ESP charge derivation and force field library building. , 2010, Physical chemistry chemical physics : PCCP.
[49] Oren A Scherman,et al. Release of high-energy water as an essential driving force for the high-affinity binding of cucurbit[n]urils. , 2012, Journal of the American Chemical Society.
[50] M. Parrinello,et al. Canonical sampling through velocity rescaling. , 2007, The Journal of chemical physics.
[51] David L Mobley,et al. Charge asymmetries in hydration of polar solutes. , 2008, The journal of physical chemistry. B.
[52] A. Warshel,et al. EFFECT OF SOLVENT DISCRETENESS ON SOLVATION , 1998 .
[53] Emilio Gallicchio,et al. The AGBNP2 Implicit Solvation Model. , 2009, Journal of chemical theory and computation.
[54] J A McCammon,et al. Coupling hydrophobicity, dispersion, and electrostatics in continuum solvent models. , 2005, Physical review letters.
[55] Ray Luo,et al. How well does Poisson-Boltzmann implicit solvent agree with explicit solvent? A quantitative analysis. , 2006, The journal of physical chemistry. B.
[56] B. Honig,et al. Calculation of the total electrostatic energy of a macromolecular system: Solvation energies, binding energies, and conformational analysis , 1988, Proteins.
[57] M K Gilson,et al. Theory of electrostatic interactions in macromolecules. , 1995, Current opinion in structural biology.
[58] C. Brooks,et al. Recent advances in the development and application of implicit solvent models in biomolecule simulations. , 2004, Current opinion in structural biology.
[59] 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.
[60] David L Mobley,et al. Comparison of charge models for fixed-charge force fields: small-molecule hydration free energies in explicit solvent. , 2007, The journal of physical chemistry. B.
[61] Andrew T. Fenley,et al. Charge hydration asymmetry: the basic principle and how to use it to test and improve water models. , 2012, The journal of physical chemistry. B.
[62] Michael R. Shirts,et al. Solvation free energies of amino acid side chain analogs for common molecular mechanics water models. , 2005, The Journal of chemical physics.
[63] G. Chang,et al. Macromodel—an integrated software system for modeling organic and bioorganic molecules using molecular mechanics , 1990 .
[64] Arieh Warshel,et al. CONTINUUM AND DIPOLE-LATTICE MODELS OF SOLVATION , 1997 .
[65] Patrice Koehl,et al. Incorporating dipolar solvents with variable density in Poisson-Boltzmann electrostatics. , 2008, Biophysical journal.
[66] Michael K Gilson,et al. Grid inhomogeneous solvation theory: hydration structure and thermodynamics of the miniature receptor cucurbit[7]uril. , 2012, The Journal of chemical physics.
[67] Patrice Koehl,et al. Beyond the Poisson-Boltzmann model: modeling biomolecule-water and water-water interactions. , 2009, Physical review letters.
[68] P. Kollman,et al. Settle: An analytical version of the SHAKE and RATTLE algorithm for rigid water models , 1992 .
[69] B. Montgomery Pettitt,et al. Electrostatic solvation free energy of amino acid side chain analogs: Implications for the validity of electrostatic linear response in water , 2011, J. Comput. Chem..
[70] Lyle Isaacs,et al. The cucurbit[n]uril family: prime components for self-sorting systems. , 2005, Journal of the American Chemical Society.
[71] W. Im,et al. Continuum solvation model: Computation of electrostatic forces from numerical solutions to the Poisson-Boltzmann equation , 1998 .
[72] M. Gilson,et al. Calculation of protein-ligand binding affinities. , 2007, Annual review of biophysics and biomolecular structure.
[73] C. Chipot,et al. FREE ENERGY CALCULATIONS OF WATSON-CRICK BASE PAIRING IN AQUEOUS SOLUTION , 1999 .
[74] Charles L Brooks,et al. Implicit modeling of nonpolar solvation for simulating protein folding and conformational transitions. , 2008, Physical chemistry chemical physics : PCCP.
[75] S. Hassan. Self-consistent treatment of the local dielectric permittivity and electrostatic potential in solution for polarizable macromolecular force fields. , 2012, The Journal of chemical physics.
[76] R. Levy,et al. Computer simulations with explicit solvent: recent progress in the thermodynamic decomposition of free energies and in modeling electrostatic effects. , 1998, Annual review of physical chemistry.
[77] Andrew T. Fenley,et al. Entropy–enthalpy transduction caused by conformational shifts can obscure the forces driving protein–ligand binding , 2012, Proceedings of the National Academy of Sciences.
[78] Michael R. Shirts,et al. Extremely precise free energy calculations of amino acid side chain analogs: Comparison of common molecular mechanics force fields for proteins , 2003 .
[79] C. Brooks,et al. Novel generalized Born methods , 2002 .
[80] Traian Sulea,et al. Restoring charge asymmetry in continuum electrostatics calculations of hydration free energies. , 2009, The journal of physical chemistry. B.
[81] César Augusto F. de Oliveira,et al. On the Role of Dewetting Transitions in Host–Guest Binding Free Energy Calculations , 2012, Journal of chemical theory and computation.