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300 related items for PubMed ID: 1782354

  • 1. A molecular dynamics study of thermodynamic and structural aspects of the hydration of cavities in proteins.
    Wade RC, Mazor MH, McCammon JA, Quiocho FA.
    Biopolymers; 1991 Jul; 31(8):919-31. PubMed ID: 1782354
    [Abstract] [Full Text] [Related]

  • 2. Absolute and relative binding free energy calculations of the interaction of biotin and its analogs with streptavidin using molecular dynamics/free energy perturbation approaches.
    Miyamoto S, Kollman PA.
    Proteins; 1993 Jul; 16(3):226-45. PubMed ID: 8346190
    [Abstract] [Full Text] [Related]

  • 3. Hydration energy landscape of the active site cavity in cytochrome P450cam.
    Helms V, Wade RC.
    Proteins; 1998 Aug 15; 32(3):381-96. PubMed ID: 9715913
    [Abstract] [Full Text] [Related]

  • 4. Free energy, entropy, and enthalpy of a water molecule in various protein environments.
    Yu H, Rick SW.
    J Phys Chem B; 2010 Sep 09; 114(35):11552-60. PubMed ID: 20704188
    [Abstract] [Full Text] [Related]

  • 5. Mechanism of the hydration of carbon dioxide: direct participation of H2O versus microsolvation.
    Nguyen MT, Matus MH, Jackson VE, Vu TN, Rustad JR, Dixon DA.
    J Phys Chem A; 2008 Oct 16; 112(41):10386-98. PubMed ID: 18816037
    [Abstract] [Full Text] [Related]

  • 6. Electrostatic polarization effects and hydrophobic hydration in ethanol-water solutions from molecular dynamics simulations.
    Zhong Y, Patel S.
    J Phys Chem B; 2009 Jan 22; 113(3):767-78. PubMed ID: 19115819
    [Abstract] [Full Text] [Related]

  • 7. Determination of the differential effects of hydrogen bonding and water release on the binding of FK506 to native and Tyr82-->Phe82 FKBP-12 proteins using free energy simulations.
    Pearlman DA, Connelly PR.
    J Mol Biol; 1995 May 05; 248(3):696-717. PubMed ID: 7538591
    [Abstract] [Full Text] [Related]

  • 8. Classification of water molecules in protein binding sites.
    Barillari C, Taylor J, Viner R, Essex JW.
    J Am Chem Soc; 2007 Mar 07; 129(9):2577-87. PubMed ID: 17288418
    [Abstract] [Full Text] [Related]

  • 9. Determination of protein surface hydration shell free energy of water motion: theoretical study and molecular dynamics simulation.
    Sheu SY, Yang DY.
    J Phys Chem B; 2010 Dec 16; 114(49):16558-66. PubMed ID: 21090707
    [Abstract] [Full Text] [Related]

  • 10. Molecular dynamics study of water penetration in staphylococcal nuclease.
    Damjanović A, García-Moreno B, Lattman EE, García AE.
    Proteins; 2005 Aug 15; 60(3):433-49. PubMed ID: 15971206
    [Abstract] [Full Text] [Related]

  • 11. Hydration of a hydrophobic cavity and its functional role: a simulation study of human interleukin-1beta.
    Somani S, Chng CP, Verma CS.
    Proteins; 2007 Jun 01; 67(4):868-85. PubMed ID: 17380484
    [Abstract] [Full Text] [Related]

  • 12. Mapping the energetics of water-protein and water-ligand interactions with the "natural" HINT forcefield: predictive tools for characterizing the roles of water in biomolecules.
    Amadasi A, Spyrakis F, Cozzini P, Abraham DJ, Kellogg GE, Mozzarelli A.
    J Mol Biol; 2006 Apr 21; 358(1):289-309. PubMed ID: 16497327
    [Abstract] [Full Text] [Related]

  • 13. Hydrophilicity of cavities in proteins.
    Zhang L, Hermans J.
    Proteins; 1996 Apr 21; 24(4):433-8. PubMed ID: 9162944
    [Abstract] [Full Text] [Related]

  • 14. Standard free energy of releasing a localized water molecule from the binding pockets of proteins: double-decoupling method.
    Hamelberg D, McCammon JA.
    J Am Chem Soc; 2004 Jun 23; 126(24):7683-9. PubMed ID: 15198616
    [Abstract] [Full Text] [Related]

  • 15. Entropy of water in the hydration layer of major and minor grooves of DNA.
    Jana B, Pal S, Maiti PK, Lin ST, Hynes JT, Bagchi B.
    J Phys Chem B; 2006 Oct 05; 110(39):19611-8. PubMed ID: 17004828
    [Abstract] [Full Text] [Related]

  • 16. Carbohydrate-binding proteins: Dissecting ligand structures through solvent environment occupancy.
    Gauto DF, Di Lella S, Guardia CM, Estrin DA, Martí MA.
    J Phys Chem B; 2009 Jun 25; 113(25):8717-24. PubMed ID: 19485380
    [Abstract] [Full Text] [Related]

  • 17. 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
    [Abstract] [Full Text] [Related]

  • 18. Treatment of dilute clusters of methanol and water by ab initio quantum mechanical calculations.
    Ruckenstein E, Shulgin IL, Tilson JL.
    J Phys Chem A; 2005 Feb 10; 109(5):807-15. PubMed ID: 16838951
    [Abstract] [Full Text] [Related]

  • 19. Theoretical analysis on changes in thermodynamic quantities upon protein folding: essential role of hydration.
    Imai T, Harano Y, Kinoshita M, Kovalenko A, Hirata F.
    J Chem Phys; 2007 Jun 14; 126(22):225102. PubMed ID: 17581082
    [Abstract] [Full Text] [Related]

  • 20. The hydration of globular proteins as derived from volume and compressibility measurements: cross correlating thermodynamic and structural data.
    Chalikian TV, Totrov M, Abagyan R, Breslauer KJ.
    J Mol Biol; 1996 Jul 26; 260(4):588-603. PubMed ID: 8759322
    [Abstract] [Full Text] [Related]

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