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742 related items for PubMed ID: 17119645

  • 1. Calculations of solute and solvent entropies from molecular dynamics simulations.
    Carlsson J, Aqvist J.
    Phys Chem Chem Phys; 2006 Dec 14; 8(46):5385-95. PubMed ID: 17119645
    [Abstract] [Full Text] [Related]

  • 2. Absolute hydration entropies of alkali metal ions from molecular dynamics simulations.
    Carlsson J, Aqvist J.
    J Phys Chem B; 2009 Jul 30; 113(30):10255-60. PubMed ID: 19580304
    [Abstract] [Full Text] [Related]

  • 3. Absolute and relative entropies from computer simulation with applications to ligand binding.
    Carlsson J, Aqvist J.
    J Phys Chem B; 2005 Apr 07; 109(13):6448-56. PubMed ID: 16851719
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  • 4. Examining methods for calculations of binding free energies: LRA, LIE, PDLD-LRA, and PDLD/S-LRA calculations of ligands binding to an HIV protease.
    Sham YY, Chu ZT, Tao H, Warshel A.
    Proteins; 2000 Jun 01; 39(4):393-407. PubMed ID: 10813821
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  • 5. Discrimination between native and intentionally misfolded conformations of proteins: ES/IS, a new method for calculating conformational free energy that uses both dynamics simulations with an explicit solvent and an implicit solvent continuum model.
    Vorobjev YN, Almagro JC, Hermans J.
    Proteins; 1998 Sep 01; 32(4):399-413. PubMed ID: 9726412
    [Abstract] [Full Text] [Related]

  • 6. Unraveling water's entropic mysteries: a unified view of nonpolar, polar, and ionic hydration.
    Ben-Amotz D, Underwood R.
    Acc Chem Res; 2008 Aug 01; 41(8):957-67. PubMed ID: 18710198
    [Abstract] [Full Text] [Related]

  • 7. Influence of the solvent representation on vibrational entropy calculations: generalized born versus distance-dependent dielectric model.
    Kopitz H, Cashman DA, Pfeiffer-Marek S, Gohlke H.
    J Comput Chem; 2012 Apr 05; 33(9):1004-13. PubMed ID: 22298332
    [Abstract] [Full Text] [Related]

  • 8. (Thermo)dynamic role of receptor flexibility, entropy, and motional correlation in protein-ligand binding.
    Baron R, McCammon JA.
    Chemphyschem; 2008 May 16; 9(7):983-8. PubMed ID: 18418822
    [Abstract] [Full Text] [Related]

  • 9. Loss of translational entropy in molecular associations.
    Siebert X, Amzel LM.
    Proteins; 2004 Jan 01; 54(1):104-15. PubMed ID: 14705027
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  • 10. Solvated interaction energy (SIE) for scoring protein-ligand binding affinities. 1. Exploring the parameter space.
    Naïm M, Bhat S, Rankin KN, Dennis S, Chowdhury SF, Siddiqi I, Drabik P, Sulea T, Bayly CI, Jakalian A, Purisima EO.
    J Chem Inf Model; 2007 Jan 01; 47(1):122-33. PubMed ID: 17238257
    [Abstract] [Full Text] [Related]

  • 11. Entropic cost of protein-ligand binding and its dependence on the entropy in solution.
    Irudayam SJ, Henchman RH.
    J Phys Chem B; 2009 Apr 30; 113(17):5871-84. PubMed ID: 19351118
    [Abstract] [Full Text] [Related]

  • 12. Calculation of relative binding free energies and configurational entropies: a structural and thermodynamic analysis of the nature of non-polar binding of thrombin inhibitors based on hirudin55-65.
    Wang J, Szewczuk Z, Yue SY, Tsuda Y, Konishi Y, Purisima EO.
    J Mol Biol; 1995 Oct 27; 253(3):473-92. PubMed ID: 7473728
    [Abstract] [Full Text] [Related]

  • 13. Estimating entropies from molecular dynamics simulations.
    Peter C, Oostenbrink C, van Dorp A, van Gunsteren WF.
    J Chem Phys; 2004 Feb 08; 120(6):2652-61. PubMed ID: 15268408
    [Abstract] [Full Text] [Related]

  • 14. Estimation of absolute solvent and solvation shell entropies via permutation reduction.
    Reinhard F, Grubmüller H.
    J Chem Phys; 2007 Jan 07; 126(1):014102. PubMed ID: 17212485
    [Abstract] [Full Text] [Related]

  • 15. Incorporating receptor flexibility in the molecular design of protein interfaces.
    Li L, Liang S, Pilcher MM, Meroueh SO.
    Protein Eng Des Sel; 2009 Sep 07; 22(9):575-86. PubMed ID: 19643976
    [Abstract] [Full Text] [Related]

  • 16. Estimation of changes in side chain configurational entropy in binding and folding: general methods and application to helix formation.
    Lee KH, Xie D, Freire E, Amzel LM.
    Proteins; 1994 Sep 07; 20(1):68-84. PubMed ID: 7824524
    [Abstract] [Full Text] [Related]

  • 17. Confusing cause and effect: energy-entropy compensation in the preferential solvation of a nonpolar solute in dimethyl sulfoxide/water mixtures.
    Ozal TA, van der Vegt NF.
    J Phys Chem B; 2006 Jun 22; 110(24):12104-12. PubMed ID: 16800523
    [Abstract] [Full Text] [Related]

  • 18. On the nonpolar hydration free energy of proteins: surface area and continuum solvent models for the solute-solvent interaction energy.
    Levy RM, Zhang LY, Gallicchio E, Felts AK.
    J Am Chem Soc; 2003 Aug 06; 125(31):9523-30. PubMed ID: 12889983
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  • 19. Calculations of pH-dependent binding of proteins to biological membranes.
    Mihajlovic M, Lazaridis T.
    J Phys Chem B; 2006 Feb 23; 110(7):3375-84. PubMed ID: 16494352
    [Abstract] [Full Text] [Related]

  • 20. Calculation of configurational entropy with a Boltzmann-quasiharmonic model: the origin of high-affinity protein-ligand binding.
    Harpole KW, Sharp KA.
    J Phys Chem B; 2011 Aug 04; 115(30):9461-72. PubMed ID: 21678965
    [Abstract] [Full Text] [Related]

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