An effective solvation term based on atomic occupancies for use in protein simulations
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[1] W. Kauzmann. Some factors in the interpretation of protein denaturation. , 1959, Advances in protein chemistry.
[2] C. Chothia,et al. Hydrophobic bonding and accessible surface area in proteins , 1974, Nature.
[3] M. Karplus,et al. Dynamics of folded proteins , 1977, Nature.
[4] G J Williams,et al. The Protein Data Bank: a computer-based archival file for macromolecular structures. , 1977, Journal of molecular biology.
[5] M. Perutz. Electrostatic effects in proteins. , 1978, Science.
[6] P. Gianni,et al. Thermodynamic functions of hydration of saturated uncharged organic compounds. Free energies, enthalpies and entropies at 25°C , 1979 .
[7] P M Cullis,et al. Affinities of amino acid side chains for solvent water. , 1981, Biochemistry.
[8] J. Israelachvili,et al. The hydrophobic interaction is long range, decaying exponentially with distance , 1982, Nature.
[9] J. Warwicker,et al. Calculation of the electric potential in the active site cleft due to alpha-helix dipoles. , 1982, Journal of molecular biology.
[10] W. Kabsch,et al. Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical features , 1983, Biopolymers.
[11] E. Gratton,et al. Water and globular proteins , 1983 .
[12] E. Baker,et al. Hydrogen bonding in globular proteins. , 1984, Progress in biophysics and molecular biology.
[13] B. Honig,et al. Stability of "salt bridges" in membrane proteins. , 1984, Proceedings of the National Academy of Sciences of the United States of America.
[14] C. Frömmel,et al. The apolar surface area of amino acids and its empirical correlation with hydrophobic free energy. , 1984, Journal of theoretical biology.
[15] Garland R. Marshall,et al. Van der Waals volume fragmental constants , 1985 .
[16] J. Israelachvili. Intermolecular and surface forces , 1985 .
[17] A. D. McLachlan,et al. Solvation energy in protein folding and binding , 1986, Nature.
[18] T. Straatsma,et al. THE MISSING TERM IN EFFECTIVE PAIR POTENTIALS , 1987 .
[19] Haruki Nakamura,et al. Numerical Calculations of Electrostatic Potentials of Protein-Solvent Systems by the Self Consistent Boundary Method , 1987 .
[20] S. Yip,et al. Molecular dynamics simulation of dielectric properties of water , 1987 .
[21] H. Scheraga,et al. Accessible surface areas as a measure of the thermodynamic parameters of hydration of peptides. , 1987, Proceedings of the National Academy of Sciences of the United States of America.
[22] M. Oobatake,et al. Effects of hydrated water on protein unfolding. , 1988, Journal of biochemistry.
[23] R. Sharon,et al. Accurate simulation of protein dynamics in solution. , 1988, Proceedings of the National Academy of Sciences of the United States of America.
[24] B. Honig,et al. Calculation of the total electrostatic energy of a macromolecular system: Solvation energies, binding energies, and conformational analysis , 1988, Proteins.
[25] H. Berendsen,et al. A LEAP-FROG ALGORITHM FOR STOCHASTIC DYNAMICS , 1988 .
[26] Wang Lu,et al. ON THE APPROXIMATION OF SOLVENT EFFECTS ON THE CONFORMATION AND DYNAMICS OF CYCLOSPORIN A BY STOCHASTIC DYNAMICS SIMULATION TECHNIQUES , 1988 .
[27] P. Privalov,et al. Stability of protein structure and hydrophobic interaction. , 1988, Advances in protein chemistry.
[28] K. Sharp,et al. Calculating the electrostatic potential of molecules in solution: Method and error assessment , 1988 .
[29] Harold A. Scheraga,et al. Free energies of hydration of solute molecules. IV: Revised treatment of the hydration shell model , 1988 .
[30] Arieh Warshel,et al. A surface constrained all‐atom solvent model for effective simulations of polar solutions , 1989 .
[31] C Sander,et al. Polarity as a criterion in protein design. , 1989, Protein engineering.
[32] J. Rullmann,et al. The active site of papain. All-atom study of interactions with protein matrix and solvent. , 1989, Journal of molecular biology.
[33] M. Karplus,et al. pKa's of ionizable groups in proteins: atomic detail from a continuum electrostatic model. , 1990, Biochemistry.
[34] C Sander,et al. Excluded volume approximation to protein-solvent interaction. The solvent contact model. , 1990, Biophysical journal.
[35] G Vriend,et al. WHAT IF: a molecular modeling and drug design program. , 1990, Journal of molecular graphics.
[36] M. Schaefer,et al. A precise analytical method for calculating the electrostatic energy of macromolecules in aqueous solution. , 1990, Journal of molecular biology.
[37] W. C. Still,et al. Semianalytical treatment of solvation for molecular mechanics and dynamics , 1990 .
[38] K A Dill,et al. Decisions in force field development: an alternative to those described by Roterman et al. (J. Biomol. Struct. Dyn. 7, 421 (1989)). , 1991, Journal of biomolecular structure & dynamics.
[39] B Honig,et al. Extracting hydrophobic free energies from experimental data: relationship to protein folding and theoretical models. , 1991, Biochemistry.
[40] Anna Tempczyk,et al. Electrostatic contributions to solvation energies: comparison of free energy perturbation and continuum calculations , 1991 .
[41] Kim A. Sharp,et al. Incorporating solvent and ion screening into molecular dynamics using the finite‐difference Poisson–Boltzmann method , 1991 .
[42] Prediction of the thermodynamics of protein unfolding: the helix-coil transition of poly(L-alanine). , 1991, Proceedings of the National Academy of Sciences of the United States of America.
[43] K. Dill,et al. Protein stability: electrostatics and compact denatured states. , 1991, Proceedings of the National Academy of Sciences of the United States of America.
[44] W F van Gunsteren,et al. On the interpretation of biochemical data by molecular dynamics computer simulation. , 1992, European journal of biochemistry.
[45] Haruki Nakamura,et al. Electrostatic forces in two lysozymes: Calculations and measurements of histidine pKa values , 1992, Biopolymers.
[46] Klaus Schulten,et al. Molecular Dynamics Simulations in Heterogeneous Dielectrica and Debye-Hückel Media - Application to the Protein Bovine Pancreatic Trypsin Inhibitor , 1992 .
[47] R M Stroud,et al. Inclusion of solvation free energy with molecular mechanics energy: Alanyl dipeptide as a test case , 1992, Protein science : a publication of the Protein Society.
[48] Haruki Nakamura,et al. Presto(protein Engineering Simulator): A Vectorized Molecular Mechanics Program for Biopolymers , 1992, Comput. Chem..
[49] M Levitt,et al. Molecular dynamics simulations of helix denaturation. , 1992, Journal of molecular biology.
[50] D. Eisenberg,et al. Atomic solvation parameters applied to molecular dynamics of proteins in solution , 1992, Protein science : a publication of the Protein Society.