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265 related items for PubMed ID: 26626834

  • 1. Calculation of Standard Binding Free Energies:  Aromatic Molecules in the T4 Lysozyme L99A Mutant.
    Deng Y, Roux B.
    J Chem Theory Comput; 2006 Sep; 2(5):1255-73. PubMed ID: 26626834
    [Abstract] [Full Text] [Related]

  • 2. 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; 23(2):128-41. PubMed ID: 20151411
    [Abstract] [Full Text] [Related]

  • 3. CHARMM-GUI Ligand Binder for absolute binding free energy calculations and its application.
    Jo S, Jiang W, Lee HS, Roux B, Im W.
    J Chem Inf Model; 2013 Jan 28; 53(1):267-77. PubMed ID: 23205773
    [Abstract] [Full Text] [Related]

  • 4. Absolute binding free energy calculations using molecular dynamics simulations with restraining potentials.
    Wang J, Deng Y, Roux B.
    Biophys J; 2006 Oct 15; 91(8):2798-814. PubMed ID: 16844742
    [Abstract] [Full Text] [Related]

  • 5. Density functional theory calculations on entire proteins for free energies of binding: application to a model polar binding site.
    Fox SJ, Dziedzic J, Fox T, Tautermann CS, Skylaris CK.
    Proteins; 2014 Dec 15; 82(12):3335-46. PubMed ID: 25212393
    [Abstract] [Full Text] [Related]

  • 6. Absolute binding free energy calculations of sparsomycin analogs to the bacterial ribosome.
    Ge X, Roux B.
    J Phys Chem B; 2010 Jul 29; 114(29):9525-39. PubMed ID: 20608691
    [Abstract] [Full Text] [Related]

  • 7. Modeling protein-small molecule interactions: structure and thermodynamics of noble gases binding in a cavity in mutant phage T4 lysozyme L99A.
    Mann G, Hermans J.
    J Mol Biol; 2000 Sep 29; 302(4):979-89. PubMed ID: 10993736
    [Abstract] [Full Text] [Related]

  • 8. Charging free energy calculations using the Generalized Solvent Boundary Potential (GSBP) and periodic boundary condition: a comparative analysis using ion solvation and oxidation free energy in proteins.
    Lu X, Cui Q.
    J Phys Chem B; 2013 Feb 21; 117(7):2005-18. PubMed ID: 23347181
    [Abstract] [Full Text] [Related]

  • 9. Analysis of the binding energies of testosterone, 5alpha-dihydrotestosterone, androstenedione and dehydroepiandrosterone sulfate with an antitestosterone antibody.
    Nordman N, Valjakka J, Peräkylä M.
    Proteins; 2003 Jan 01; 50(1):135-43. PubMed ID: 12471606
    [Abstract] [Full Text] [Related]

  • 10. Protein-ligand binding free energies from exhaustive docking.
    Purisima EO, Hogues H.
    J Phys Chem B; 2012 Jun 14; 116(23):6872-9. PubMed ID: 22432509
    [Abstract] [Full Text] [Related]

  • 11. 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]

  • 12. 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 21; 16(3):226-45. PubMed ID: 8346190
    [Abstract] [Full Text] [Related]

  • 13. Fragment-based computation of binding free energies by systematic sampling.
    Clark M, Meshkat S, Talbot GT, Carnevali P, Wiseman JS.
    J Chem Inf Model; 2009 Aug 21; 49(8):1901-13. PubMed ID: 19610599
    [Abstract] [Full Text] [Related]

  • 14. 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]

  • 15. Free energies of binding from large-scale first-principles quantum mechanical calculations: application to ligand hydration energies.
    Fox SJ, Pittock C, Tautermann CS, Fox T, Christ C, Malcolm NO, Essex JW, Skylaris CK.
    J Phys Chem B; 2013 Aug 15; 117(32):9478-85. PubMed ID: 23841453
    [Abstract] [Full Text] [Related]

  • 16. Predicting ligand binding affinity with alchemical free energy methods in a polar model binding site.
    Boyce SE, Mobley DL, Rocklin GJ, Graves AP, Dill KA, Shoichet BK.
    J Mol Biol; 2009 Dec 11; 394(4):747-63. PubMed ID: 19782087
    [Abstract] [Full Text] [Related]

  • 17. Use of stabilizing mutations to engineer a charged group within a ligand-binding hydrophobic cavity in T4 lysozyme.
    Liu L, Baase WA, Michael MM, Matthews BW.
    Biochemistry; 2009 Sep 22; 48(37):8842-51. PubMed ID: 19663503
    [Abstract] [Full Text] [Related]

  • 18. Glycogen phosphorylase inhibitors: a free energy perturbation analysis of glucopyranose spirohydantoin analogues.
    Archontis G, Watson KA, Xie Q, Andreou G, Chrysina ED, Zographos SE, Oikonomakos NG, Karplus M.
    Proteins; 2005 Dec 01; 61(4):984-98. PubMed ID: 16245298
    [Abstract] [Full Text] [Related]

  • 19. Nonpolar Solvation Free Energies of Protein-Ligand Complexes.
    Genheden S, Kongsted J, Söderhjelm P, Ryde U.
    J Chem Theory Comput; 2010 Nov 09; 6(11):3558-68. PubMed ID: 26617102
    [Abstract] [Full Text] [Related]

  • 20. Grand canonical free-energy calculations of protein-ligand binding.
    Clark M, Meshkat S, Wiseman JS.
    J Chem Inf Model; 2009 Apr 09; 49(4):934-43. PubMed ID: 19309088
    [Abstract] [Full Text] [Related]

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