The Gaussian Generalized Born model: application to small molecules.
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J A Grant | J. A. Grant | B. T. Pickup | A. Nicholls | M. Sykes | B T Pickup | M J Sykes | C A Kitchen | A Nicholls | C. Kitchen
[1] A. Warshel,et al. Electrostatic effects in macromolecules: fundamental concepts and practical modeling. , 1998, Current opinion in structural biology.
[2] C. Brooks,et al. Novel generalized Born methods , 2002 .
[3] J. A. Grant,et al. A Gaussian Description of Molecular Shape , 1995 .
[4] Charles L. Brooks,et al. New analytic approximation to the standard molecular volume definition and its application to generalized Born calculations , 2003, J. Comput. Chem..
[5] G. Chang,et al. Macromodel—an integrated software system for modeling organic and bioorganic molecules using molecular mechanics , 1990 .
[6] J. Andrew Grant,et al. A smooth permittivity function for Poisson–Boltzmann solvation methods , 2001, J. Comput. Chem..
[7] Ronald M. Levy,et al. AGBNP: An analytic implicit solvent model suitable for molecular dynamics simulations and high‐resolution modeling , 2004, J. Comput. Chem..
[8] Tomasz Grycuk,et al. Deficiency of the Coulomb-field approximation in the generalized Born model: An improved formula for Born radii evaluation , 2003 .
[9] A. D. McLachlan,et al. Solvation energy in protein folding and binding , 1986, Nature.
[10] R. Friesner,et al. Generalized Born Model Based on a Surface Integral Formulation , 1998 .
[11] Harold A. Scheraga,et al. Free energies of hydration of solute molecules. 1. Improvement of the hydration shell model by exact computations of overlapping volumes , 1987 .
[12] J. A. Grant,et al. A fast method of molecular shape comparison: A simple application of a Gaussian description of molecular shape , 1996, J. Comput. Chem..
[13] S. F. Boys. Electronic wave functions - I. A general method of calculation for the stationary states of any molecular system , 1950, Proceedings of the Royal Society of London. Series A. Mathematical and Physical Sciences.
[14] Harold A. Scheraga,et al. Free energies of hydration of solute molecules. 3. Application of the hydration shell model to charged organic molecules , 1987 .
[15] Wei Yang,et al. Protein–nucleic acid interactions: from A(rgonaute) to X(PF) , 2006 .
[16] Mark Gerstein,et al. Normal modes for predicting protein motions: A comprehensive database assessment and associated Web tool , 2005, Protein science : a publication of the Protein Society.
[17] W. C. Still,et al. The GB/SA Continuum Model for Solvation. A Fast Analytical Method for the Calculation of Approximate Born Radii , 1997 .
[18] J. Gasteiger,et al. Automatic generation of 3D-atomic coordinates for organic molecules , 1990 .
[19] B. Honig,et al. Classical electrostatics in biology and chemistry. , 1995, Science.
[20] J. Warwicker,et al. Calculation of the electric potential in the active site cleft due to alpha-helix dipoles. , 1982, Journal of molecular biology.
[21] 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..
[22] M. A. Vorotyntsev,et al. Electrostatic models in the theory of solutions , 1976 .
[23] David A. Case,et al. Effective Born radii in the generalized Born approximation: The importance of being perfect , 2002, J. Comput. Chem..
[24] H. Scheraga,et al. Model for the conformational analysis of hydrated peptides. Effect of hydration on the conformational stability of the terminally blocked residues of the 20 naturally occurring amino acids , 1979 .
[25] S. Muchmore,et al. The Use of Three‐Dimensional Shape and Electrostatic Similarity Searching in the Identification of a Melanin‐Concentrating Hormone Receptor 1 Antagonist , 2006, Chemical biology & drug design.
[26] Gergely Tóth,et al. Fast protein structure prediction using Monte Carlo simulations with modal moves. , 2003, Journal of the American Chemical Society.
[27] A. Kidera,et al. Protein Motions Represented in Moving Normal Mode Coordinates , 2004 .
[28] H. Scheraga,et al. Empirical solvation models can be used to differentiate native from near‐native conformations of bovine pancreatic trypsin inhibitor , 1991, Proteins.
[29] W. Im,et al. Continuum solvation model: Computation of electrostatic forces from numerical solutions to the Poisson-Boltzmann equation , 1998 .
[30] J. Andrew McCammon,et al. Dielectric boundary smoothing in finite difference solutions of the poisson equation: An approach to improve accuracy and convergence , 1991 .
[31] Richard A. Friesner,et al. What role do surfaces play in GB models? A new‐generation of surface‐generalized born model based on a novel gaussian surface for biomolecules , 2006, J. Comput. Chem..
[32] M. Karplus,et al. A Comprehensive Analytical Treatment of Continuum Electrostatics , 1996 .
[33] Charles L. Brooks,et al. Generalized born model with a simple smoothing function , 2003, J. Comput. Chem..
[34] P. Koehl. Electrostatics calculations: latest methodological advances. , 2006, Current opinion in structural biology.
[35] J. A. Grant,et al. A shape-based 3-D scaffold hopping method and its application to a bacterial protein-protein interaction. , 2005, Journal of medicinal chemistry.
[36] Nathan A. Baker,et al. Improving implicit solvent simulations: a Poisson-centric view. , 2005, Current opinion in structural biology.
[37] W. C. Still,et al. Semianalytical treatment of solvation for molecular mechanics and dynamics , 1990 .