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211 related items for PubMed ID: 18991438

  • 1. Computation of the contribution from the cavity effect to protein-ligand binding free energy.
    Grigoriev FV, Gabin SN, Romanov AN, Sulimov VB.
    J Phys Chem B; 2008 Dec 04; 112(48):15355-60. PubMed ID: 18991438
    [Abstract] [Full Text] [Related]

  • 2. 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
    [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. 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]

  • 5. 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]

  • 6. 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
    [Abstract] [Full Text] [Related]

  • 7. 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]

  • 8. 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]

  • 9. 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]

  • 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 Sep 13; 47(1):122-33. PubMed ID: 17238257
    [Abstract] [Full Text] [Related]

  • 11. PEARLS: program for energetic analysis of receptor-ligand system.
    Han LY, Lin HH, Li ZR, Zheng CJ, Cao ZW, Xie B, Chen YZ.
    J Chem Inf Model; 2006 Sep 13; 46(1):445-50. PubMed ID: 16426079
    [Abstract] [Full Text] [Related]

  • 12. Fully automated molecular mechanics based induced fit protein-ligand docking method.
    Koska J, Spassov VZ, Maynard AJ, Yan L, Austin N, Flook PK, Venkatachalam CM.
    J Chem Inf Model; 2008 Oct 13; 48(10):1965-73. PubMed ID: 18816046
    [Abstract] [Full Text] [Related]

  • 13. 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]

  • 14. Grand canonical free-energy calculations of protein-ligand binding.
    Clark M, Meshkat S, Wiseman JS.
    J Chem Inf Model; 2009 Apr 13; 49(4):934-43. PubMed ID: 19309088
    [Abstract] [Full Text] [Related]

  • 15. Contribution of conformer focusing to the uncertainty in predicting free energies for protein-ligand binding.
    Tirado-Rives J, Jorgensen WL.
    J Med Chem; 2006 Oct 05; 49(20):5880-4. PubMed ID: 17004703
    [Abstract] [Full Text] [Related]

  • 16. Dynamic ligand design and combinatorial optimization: designing inhibitors to endothiapepsin.
    Stultz CM, Karplus M.
    Proteins; 2000 Aug 01; 40(2):258-89. PubMed ID: 10842341
    [Abstract] [Full Text] [Related]

  • 17. 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]

  • 18. Cavitation free energy for organic molecules having various sizes and shapes.
    Grigoriev FV, Basilevsky MV, Gabin SN, Romanov AN, Sulimov VB.
    J Phys Chem B; 2007 Dec 13; 111(49):13748-55. PubMed ID: 18020442
    [Abstract] [Full Text] [Related]

  • 19. Protein-ligand binding free energy calculation by the Smooth Reaction Path Generation (SRPG) Method.
    Fukunishi Y, Mitomo D, Nakamura H.
    J Chem Inf Model; 2009 Aug 13; 49(8):1944-51. PubMed ID: 19807195
    [Abstract] [Full Text] [Related]

  • 20. 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]

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