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Volume 5   Issue 2   Year 2010
Tikhonov D.A., Sobolev E.V.

Method of Pseudoaveraged Functions in the RISM Theory. Temperature Dependence of Oxytocin Peptide Hydration

Mathematical Biology & Bioinformatics. 2010;5(2):202-214.

doi: 10.17537/2010.5.202.

References

  1. Chandler D, Andersen HC. Optimized cluster expansions for classical fluids. II. Theory of molecular liquids. Journal of Chemical Physics. 1972;57:1930-1937.
  2. Tikhonov D, Sobolev E. An Averaged Over Molecular Trajectories Method of Integral Equations of the Theory of Liquids in RISM Approximation. Mathematical Biology and Bioinformatics. 2010;5(2):188-201  (in Russ.). doi: 10.17537/2010.5.188
  3. Schweizer KS, Curro JG. Integral-equation theory of the structure of polymer melts. Physical Review Letters. 1987;58(3):246-249. doi: 10.1103/PhysRevLett.58.246
  4. Hirata F, Rossky PJ, Pettitt BM. The interionic potential of mean force in a molecular polar solvent from an extended RISM equation. Journal of Chemical Physics. 1983;78(6):4133-4144. doi: 10.1063/1.445090
  5. van Leeuwen JMJ, Groeneveld J, de Boer J. New method for the calculation of the pair correlation function. I. Physica. 1959;25(7-12):792-808.
  6. Kovalenko A, Hirata F. Self-consistent description of a metal-water interface by the Kohn-Sham density functional theory and the three-dimensional reference interaction site model. Journal of Chemical Physics. 1999;110(20):10095-10112. doi: 10.1063/1.478883
  7. Tikhonov DA, Polozov RV, Timoshenko EG, Kuznetsov YuA, Gorelov AV, Dawson KA. Hydration of a B-DNA fragment in the method of atom-atom correlation functions with the reference interaction site model approximation. The Journal of Chemical Physics. 1998;109:1528-1539. doi: 10.1063/1.476704
  8. Sobolev EV, Tikhonov DA, Freedman H, Truong TN. Application of the RISM Method to Estimate the Relative Gibbs Free Energies of 4',6-Diamidino-2-phenylindole Binding Within the Minor Groove of a DNA Along Simulation Trajectory. Mathematical Biology and Bioinformatics. 2010;5(2):98-113 (in Russ.). doi: 10.17537/2010.5.98
  9. Chandler D, Singh Y, Richardson DM. Excess electrons in simple fluids. I. General equilibrium theory for classical hard sphere solvents. Journal of Chemical Physics. 1984;81(4):1975-1982. doi: 10.1063/1.447820
  10. Singer SJ, Chandler D. Free energy functions in the extended RISM approximation. Molecular Physics. 1985;55:621-625. doi: 10.1080/00268978500101591
  11. Morita T, Hiroike K. A new approach to the theory of classical fluids. I. Progress of Theor. Phys. 1960;23:1003-1027.
  12. Zichi D.A., Rossky P.J. Molecular conformational equilibria in liquids. The Journal of Chemical Physics. 1986;84(3):1712-1723. doi: 10.1063/1.450469
  13. Ten-no S. Free energy of solvation for the reference interaction site model: Critical comparison of expressions. Journal of Chemical Physics. 2001;115:3724-3731. doi: 10.1063/1.1389851
  14. Ten-no S, Iwata S. On the connection between the reference interaction site model integral equation theory and the partial wave expansion of the molecular Ornstein-Zernike equation. Journal of Chemical Physics. 1999;111:4865-4868. doi: 10.1063/1.479746
  15. Kovalenko A, Hirata F. Hydration free energy of hydrophobic solutes studied by a reference interaction site model with a repulsive bridge correction and a thermodynamic perturbation method. Journal of Chemical Physics. 2000;113:2793-2805. doi: 10.1063/1.1305885
  16. Pearlman DA, Case DA, Caldwell JW, Ross WS, Cheatham TE III, DeBolt S, Ferguson D, Seibel G, Kollman P. 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. Computational Physics Communications. 1995;91:1-41. doi: 10.1016/0010-4655(95)00041-D
  17. Case DA, Darden TA, Cheatham TE, Simmerling C, Wang J, Duke RE, Luo R, Merz KM, Pearlman DA, Crowley M et al. AMBER 9. San Francisco: University of California; 2006.
  18. Onufriev A., Bashford D., Case D.A. Modification of the Generalized Born Model Suitable for Macromolecules. Journal of Physical Chemistry B. 2000;104(15):3712-3720. doi: 10.1021/jp994072s
  19. Cornell WD, Cieplak P, Bayly CI, Gould IR, Merz KM, Ferguson DM, Spellmeyer DC, Fox T, Caldwell JW, Kollman PA. A Second Generation Force Field for the Simulation of Proteins and Nucleic Acids. Journal of the American Chemical Society. 1995;117:5179-5197. doi: 10.1021/ja00124a002
  20. Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML. Comparison of simple potential functions for simulating liquid water. Journal of Chemical Physics. 1983;79(2):926-935. doi: 10.1063/1.445869
  21. York D., Evensen N.M., Mart´ınez M.L., Delgado J.D.B. Unified equations for the slope, intercept, and standard errors of the best straight line. American Journal of Physics. 2004;72(3):367-375. doi: 10.1119/1.1632486
  22. Tikhonov DA, Sobolev EV. Estimating of the Gibbs energy of hydration from molecular dynamic trajectories obtained by integral equations of the theory of liquids in the RISM approximation. Russian Journal of Physical Chemistry. 2011;85(4):654-659. doi: 10.1134/S0036024411030307
Table of Contents Original Article
Math. Biol. Bioinf.
2010;5(2):202-214
doi: 10.17537/2010.5.202
published in Russian

Abstract (rus.)
Abstract (eng.)
Full text (rus., pdf)
References

 

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