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Journal Abstract Search

471 related items for PubMed ID: 17288418

  • 1. 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]

  • 2. 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]

  • 3. Predicting conserved water-mediated and polar ligand interactions in proteins using a K-nearest-neighbors genetic algorithm.
    Raymer ML, Sanschagrin PC, Punch WF, Venkataraman S, Goodman ED, Kuhn LA.
    J Mol Biol; 1997 Jan 31; 265(4):445-64. PubMed ID: 9034363
    [Abstract] [Full Text] [Related]

  • 4. Binding free energy contributions of interfacial waters in HIV-1 protease/inhibitor complexes.
    Lu Y, Yang CY, Wang S.
    J Am Chem Soc; 2006 Sep 13; 128(36):11830-9. PubMed ID: 16953623
    [Abstract] [Full Text] [Related]

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  • 6. 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]

  • 7. Molecular docking with ligand attached water molecules.
    Lie MA, Thomsen R, Pedersen CN, Schiøtt B, Christensen MH.
    J Chem Inf Model; 2011 Apr 25; 51(4):909-17. PubMed ID: 21452852
    [Abstract] [Full Text] [Related]

  • 8. A water-swap reaction coordinate for the calculation of absolute protein-ligand binding free energies.
    Woods CJ, Malaisree M, Hannongbua S, Mulholland AJ.
    J Chem Phys; 2011 Feb 07; 134(5):054114. PubMed ID: 21303099
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  • 10. Thermodynamic contributions of the ordered water molecule in HIV-1 protease.
    Li Z, Lazaridis T.
    J Am Chem Soc; 2003 Jun 04; 125(22):6636-7. PubMed ID: 12769565
    [Abstract] [Full Text] [Related]

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  • 12. The particle concept: placing discrete water molecules during protein-ligand docking predictions.
    Rarey M, Kramer B, Lengauer T.
    Proteins; 1999 Jan 01; 34(1):17-28. PubMed ID: 10336380
    [Abstract] [Full Text] [Related]

  • 13. Structural parameterization of the binding enthalpy of small ligands.
    Luque I, Freire E.
    Proteins; 2002 Nov 01; 49(2):181-90. PubMed ID: 12210999
    [Abstract] [Full Text] [Related]

  • 14. Molecular modeling of hydration in drug design.
    Mancera RL.
    Curr Opin Drug Discov Devel; 2007 May 01; 10(3):275-80. PubMed ID: 17554853
    [Abstract] [Full Text] [Related]

  • 15. The effect of water displacement on binding thermodynamics: concanavalin A.
    Li Z, Lazaridis T.
    J Phys Chem B; 2005 Jan 13; 109(1):662-70. PubMed ID: 16851059
    [Abstract] [Full Text] [Related]

  • 16. Strategies to calculate water binding free energies in protein-ligand complexes.
    Bodnarchuk MS, Viner R, Michel J, Essex JW.
    J Chem Inf Model; 2014 Jun 23; 54(6):1623-33. PubMed ID: 24684745
    [Abstract] [Full Text] [Related]

  • 17. De novo ligand design to an ensemble of protein structures.
    Todorov NP, Buenemann CL, Alberts IL.
    Proteins; 2006 Jul 01; 64(1):43-59. PubMed ID: 16555306
    [Abstract] [Full Text] [Related]

  • 18. Thermodynamics of buried water clusters at a protein-ligand binding interface.
    Li Z, Lazaridis T.
    J Phys Chem B; 2006 Jan 26; 110(3):1464-75. PubMed ID: 16471698
    [Abstract] [Full Text] [Related]

  • 19. Ligand-protein docking with water molecules.
    Roberts BC, Mancera RL.
    J Chem Inf Model; 2008 Feb 26; 48(2):397-408. PubMed ID: 18211049
    [Abstract] [Full Text] [Related]

  • 20. Simple, intuitive calculations of free energy of binding for protein-ligand complexes. 3. The free energy contribution of structural water molecules in HIV-1 protease complexes.
    Fornabaio M, Spyrakis F, Mozzarelli A, Cozzini P, Abraham DJ, Kellogg GE.
    J Med Chem; 2004 Aug 26; 47(18):4507-16. PubMed ID: 15317462
    [Abstract] [Full Text] [Related]

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