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167 related items for PubMed ID: 24684745

  • 1. 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]

  • 2. 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]

  • 3. 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]

  • 4. Combined quantum mechanics/molecular mechanics (QM/MM) simulations for protein-ligand complexes: free energies of binding of water molecules in influenza neuraminidase.
    Woods CJ, Shaw KE, Mulholland AJ.
    J Phys Chem B; 2015 Jan 22; 119(3):997-1001. PubMed ID: 25340313
    [Abstract] [Full Text] [Related]

  • 5. 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]

  • 6. Computation of binding free energy with molecular dynamics and grand canonical Monte Carlo simulations.
    Deng Y, Roux B.
    J Chem Phys; 2008 Mar 21; 128(11):115103. PubMed ID: 18361618
    [Abstract] [Full Text] [Related]

  • 7. Grand canonical Monte Carlo simulation of ligand-protein binding.
    Clark M, Guarnieri F, Shkurko I, Wiseman J.
    J Chem Inf Model; 2006 Mar 21; 46(1):231-42. PubMed ID: 16426059
    [Abstract] [Full Text] [Related]

  • 8. 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]

  • 9. 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]

  • 10. Scoring binding affinity of multiple ligands using implicit solvent and a single molecular dynamics trajectory: application to influenza neuraminidase.
    Bonnet P, Bryce RA.
    J Mol Graph Model; 2005 Oct 13; 24(2):147-56. PubMed ID: 16098779
    [Abstract] [Full Text] [Related]

  • 11. 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]

  • 12. Hydration properties of ligands and drugs in protein binding sites: tightly-bound, bridging water molecules and their effects and consequences on molecular design strategies.
    García-Sosa AT.
    J Chem Inf Model; 2013 Jun 24; 53(6):1388-405. PubMed ID: 23662606
    [Abstract] [Full Text] [Related]

  • 13. Water network perturbation in ligand binding: adenosine A(2A) antagonists as a case study.
    Bortolato A, Tehan BG, Bodnarchuk MS, Essex JW, Mason JS.
    J Chem Inf Model; 2013 Jul 22; 53(7):1700-13. PubMed ID: 23725291
    [Abstract] [Full Text] [Related]

  • 14. Binding energy landscape analysis helps to discriminate true hits from high-scoring decoys in virtual screening.
    Wei D, Zheng H, Su N, Deng M, Lai L.
    J Chem Inf Model; 2010 Oct 25; 50(10):1855-64. PubMed ID: 20968314
    [Abstract] [Full Text] [Related]

  • 15. Prediction of the water content in protein binding sites.
    Michel J, Tirado-Rives J, Jorgensen WL.
    J Phys Chem B; 2009 Oct 08; 113(40):13337-46. PubMed ID: 19754086
    [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. Incorporating replacement free energy of binding-site waters in molecular docking.
    Sun H, Zhao L, Peng S, Huang N.
    Proteins; 2014 Sep 25; 82(9):1765-76. PubMed ID: 24549784
    [Abstract] [Full Text] [Related]

  • 18. Calculation of the standard binding free energy of sparsomycin to the ribosomal peptidyl-transferase P-site using molecular dynamics simulations with restraining potentials.
    Ge X, Roux B.
    J Mol Recognit; 2010 Sep 25; 23(2):128-41. PubMed ID: 20151411
    [Abstract] [Full Text] [Related]

  • 19. Accurate predictions of nonpolar solvation free energies require explicit consideration of binding-site hydration.
    Genheden S, Mikulskis P, Hu L, Kongsted J, Söderhjelm P, Ryde U.
    J Am Chem Soc; 2011 Aug 24; 133(33):13081-92. PubMed ID: 21728337
    [Abstract] [Full Text] [Related]

  • 20. Infiltration of water molecules into the oseltamivir-binding site of H274Y neuraminidase mutant causes resistance to oseltamivir.
    Park JW, Jo WH.
    J Chem Inf Model; 2009 Dec 24; 49(12):2735-41. PubMed ID: 19957991
    [Abstract] [Full Text] [Related]

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