A Cavity Corrected 3D-RISM Functional for Accurate Solvation Free Energies
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Paul Labute | Jean-François Truchon | P. Labute | B. Pettitt | Jean-François Truchon | B. Montgomery Pettitt | B. Pettitt
[1] J. Andrew Grant,et al. A smooth permittivity function for Poisson–Boltzmann solvation methods , 2001, J. Comput. Chem..
[2] B. Pettitt,et al. An Integral Equation Study of the Hydrophobic Interaction between Graphene Plates. , 2008, Journal of chemical theory and computation.
[3] 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.
[4] Peter A. Kollman,et al. A new method for carrying out free energy perturbation calculations: Dynamically modified windows , 1989 .
[5] Andriy Kovalenko,et al. An MM/3D-RISM approach for ligand binding affinities. , 2010, The journal of physical chemistry. B.
[6] Irwin D Kuntz,et al. Estimation of Absolute Free Energies of Hydration Using Continuum Methods: Accuracy of Partial Charge Models and Optimization of Nonpolar Contributions , 2022 .
[7] F. Hirata,et al. Three-dimensional density profiles of water in contact with a solute of arbitrary shape: a RISM approach , 1998 .
[8] Fumio Hirata,et al. Potentials of mean force of simple ions in ambient aqueous solution. I. Three-dimensional reference interaction site model approach , 2000 .
[9] Fumio Hirata,et al. Potentials of mean force of simple ions in ambient aqueous solution. II. Solvation structure from the three-dimensional reference interaction site model approach, and comparison with simulations , 2000 .
[10] J. Kirkwood. Statistical Mechanics of Fluid Mixtures , 1935 .
[11] Benoît Roux,et al. An Integral Equation To Describe the Solvation of Polar Molecules in Liquid Water , 1997 .
[12] Seiichiro Ten-no,et al. Comparative study on solvation free energy expressions in reference interaction site model integral equation theory. , 2005, The journal of physical chemistry. B.
[13] R. Wade,et al. New hydrogen-bond potentials for use in determining energetically favorable binding sites on molecules of known structure. , 1989, Journal of medicinal chemistry.
[14] 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 .
[15] K. Ng. Hypernetted chain solutions for the classical one‐component plasma up to Γ=7000 , 1974 .
[16] B. Montgomery Pettitt,et al. Optimized theory for simple and molecular fluids. , 2007, The Journal of chemical physics.
[17] B. Montgomery Pettitt,et al. Integral equation predictions of liquid state structure for waterlike intermolecular potentials , 1982 .
[18] W. L. Jorgensen,et al. Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids , 1996 .
[19] Fumio Hirata,et al. Potential of Mean Force between Two Molecular Ions in a Polar Molecular Solvent: A Study by the Three-Dimensional Reference Interaction Site Model , 1999 .
[20] K. Sharp,et al. Electrostatic interactions in macromolecules: theory and applications. , 1990, Annual review of biophysics and biophysical chemistry.
[21] Fumio Hirata,et al. Hydration free energy of hydrophobic solutes studied by a reference interaction site model with a repulsive bridge correction and a thermodynamic perturbation method , 2000 .
[22] David L Mobley,et al. Charge asymmetries in hydration of polar solutes. , 2008, The journal of physical chemistry. B.
[23] Carlos Simmerling,et al. Three-dimensional molecular theory of solvation coupled with molecular dynamics in Amber. , 2010, Journal of chemical theory and computation.
[24] B. Pettitt,et al. Integral Equations in the Study of Polar and Ionic Interaction Site Fluids , 2011, Journal of statistical physics.
[25] Shan Zhao,et al. Variational approach for nonpolar solvation analysis. , 2012, The Journal of chemical physics.
[26] David Chandler,et al. Free energy functions in the extended RISM approximation , 1985 .
[27] 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.
[28] S. T. Buckland,et al. An Introduction to the Bootstrap. , 1994 .
[29] K. Sharp,et al. Accurate Calculation of Hydration Free Energies Using Macroscopic Solvent Models , 1994 .
[30] R. Zwanzig. High‐Temperature Equation of State by a Perturbation Method. I. Nonpolar Gases , 1954 .
[31] Li-Tien Cheng,et al. Evaluation of Hydration Free Energy by Level-Set Variational Implicit-Solvent Model with Coulomb-Field Approximation , 2013, Journal of chemical theory and computation.
[32] P. A. Bash,et al. Free energy calculations by computer simulation. , 1987, Science.
[33] Nathan A. Baker,et al. Solvation forces on biomolecular structures: A comparison of explicit solvent and Poisson–Boltzmann models , 2004, J. Comput. Chem..
[34] I. R. Mcdonald,et al. Theory of simple liquids , 1998 .
[35] Seiichiro Ten-no,et al. Free energy of solvation for the reference interaction site model: Critical comparison of expressions , 2001 .
[36] B. Honig,et al. Calculation of the total electrostatic energy of a macromolecular system: Solvation energies, binding energies, and conformational analysis , 1988, Proteins.
[37] 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.
[38] George M. Whitesides,et al. Mechanism of the hydrophobic effect in the biomolecular recognition of arylsulfonamides by carbonic anhydrase , 2011, Proceedings of the National Academy of Sciences.
[39] B Honig,et al. Correlating solvation free energies and surface tensions of hydrocarbon solutes. , 1994, Biophysical chemistry.
[40] Christopher I. Bayly,et al. Fast, efficient generation of high‐quality atomic charges. AM1‐BCC model: II. Parameterization and validation , 2002, J. Comput. Chem..
[41] Benoît Roux,et al. Integrated Continuum Dielectric Approaches to treat Molecular Polarizability and the Condensed Phase: Refractive Index and Implicit Solvation. , 2009, Journal of chemical theory and computation.
[42] 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 .
[43] 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.
[44] G. Stell. Self-consistent equations for the radial distribution function , 1969 .
[45] T. Truong,et al. Thermochemistry of solvation: A self-consistent three-dimensional reference interaction site model approach , 2000 .
[46] Fumio Hirata,et al. Molecular Theory of Solvation , 2004 .
[47] Maxim V Fedorov,et al. Towards a universal method for calculating hydration free energies: a 3D reference interaction site model with partial molar volume correction , 2010, Journal of physics. Condensed matter : an Institute of Physics journal.
[48] Sheldon Dennis,et al. Prediction of SAMPL-1 hydration free energies using a continuum electrostatics-dispersion model. , 2009, The journal of physical chemistry. B.
[49] Nathan A. Baker,et al. Assessing implicit models for nonpolar mean solvation forces: the importance of dispersion and volume terms. , 2006, Proceedings of the National Academy of Sciences of the United States of America.
[50] B. Roux,et al. Solvation Free Energy of Polar and Nonpolar Molecules in Water: An Extended Interaction Site Integral Equation Theory in Three Dimensions , 2000 .
[51] Woody Sherman,et al. Contribution of Explicit Solvent Effects to the Binding Affinity of Small‐Molecule Inhibitors in Blood Coagulation Factor Serine Proteases , 2011, ChemMedChem.
[52] Robert Abel,et al. Motifs for molecular recognition exploiting hydrophobic enclosure in protein–ligand binding , 2007, Proceedings of the National Academy of Sciences.
[53] Charles W. Kehoe,et al. Oil/water transfer is partly driven by molecular shape, not just size. , 2010, Journal of the American Chemical Society.
[54] B. Montgomery Pettitt,et al. A dielectrically consistent interaction site theory for solvent—electrolyte mixtures , 1992 .
[55] M. Pastor,et al. A strategy for the incorporation of water molecules present in a ligand binding site into a three-dimensional quantitative structure--activity relationship analysis. , 1997, Journal of medicinal chemistry.
[56] 宁北芳,et al. 疟原虫var基因转换速率变化导致抗原变异[英]/Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A , 2005 .
[57] David Chandler,et al. Optimized Cluster Expansions for Classical Fluids. II. Theory of Molecular Liquids , 1972 .
[58] Paul Labute,et al. The generalized Born/volume integral implicit solvent model: Estimation of the free energy of hydration using London dispersion instead of atomic surface area , 2008, J. Comput. Chem..
[59] P. Goodford. A computational procedure for determining energetically favorable binding sites on biologically important macromolecules. , 1985, Journal of medicinal chemistry.