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678 related items for PubMed ID: 12889983

  • 1. 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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  • 2. AGBNP: an analytic implicit solvent model suitable for molecular dynamics simulations and high-resolution modeling.
    Gallicchio E, Levy RM.
    J Comput Chem; 2004 Mar 06; 25(4):479-99. PubMed ID: 14735568
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  • 3. The SGB/NP hydration free energy model based on the surface generalized born solvent reaction field and novel nonpolar hydration free energy estimators.
    Gallicchio E, Zhang LY, Levy RM.
    J Comput Chem; 2002 Apr 15; 23(5):517-29. PubMed ID: 11948578
    [Abstract] [Full Text] [Related]

  • 4. 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
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  • 5. Free energy landscape of protein folding in water: explicit vs. implicit solvent.
    Zhou R.
    Proteins; 2003 Nov 01; 53(2):148-61. PubMed ID: 14517967
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  • 8. Molecular dynamics simulations of peptides and proteins with a continuum electrostatic model based on screened Coulomb potentials.
    Hassan SA, Mehler EL, Zhang D, Weinstein H.
    Proteins; 2003 Apr 01; 51(1):109-25. PubMed ID: 12596268
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  • 10. Modeling loop reorganization free energies of acetylcholinesterase: a comparison of explicit and implicit solvent models.
    Olson MA.
    Proteins; 2004 Dec 01; 57(4):645-50. PubMed ID: 15481087
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  • 11. Prediction of SAMPL-1 hydration free energies using a continuum electrostatics-dispersion model.
    Sulea T, Wanapun D, Dennis S, Purisima EO.
    J Phys Chem B; 2009 Apr 09; 113(14):4511-20. PubMed ID: 19267492
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  • 12. Hydration in discrete water. A mean field, cellular automata based approach to calculating hydration free energies.
    Setny P, Zacharias M.
    J Phys Chem B; 2010 Jul 08; 114(26):8667-75. PubMed ID: 20552986
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  • 13. Implicit nonpolar solvent models.
    Tan C, Tan YH, Luo R.
    J Phys Chem B; 2007 Oct 25; 111(42):12263-74. PubMed ID: 17918880
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  • 14. Application of the level-set method to the implicit solvation of nonpolar molecules.
    Cheng LT, Dzubiella J, McCammon JA, Li B.
    J Chem Phys; 2007 Aug 28; 127(8):084503. PubMed ID: 17764265
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  • 16. Incorporating receptor flexibility in the molecular design of protein interfaces.
    Li L, Liang S, Pilcher MM, Meroueh SO.
    Protein Eng Des Sel; 2009 Sep 28; 22(9):575-86. PubMed ID: 19643976
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  • 19. Replica exchange molecular dynamics simulations of coarse-grained proteins in implicit solvent.
    Chebaro Y, Dong X, Laghaei R, Derreumaux P, Mousseau N.
    J Phys Chem B; 2009 Jan 08; 113(1):267-74. PubMed ID: 19067549
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  • 20. Solvation free energies of amino acid side chain analogs for common molecular mechanics water models.
    Shirts MR, Pande VS.
    J Chem Phys; 2005 Apr 01; 122(13):134508. PubMed ID: 15847482
    [Abstract] [Full Text] [Related]

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