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241 related items for PubMed ID: 20608691

  • 1. 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]

  • 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 Jul 29; 23(2):128-41. PubMed ID: 20151411
    [Abstract] [Full Text] [Related]

  • 3. 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]

  • 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
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  • 5. Absolute free energies of binding of peptide analogs to the HIV-1 protease from molecular dynamics simulations.
    Bartels C, Widmer A, Ehrhardt C.
    J Comput Chem; 2005 Sep 15; 26(12):1294-305. PubMed ID: 15981257
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  • 6. 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 15; 16(3):226-45. PubMed ID: 8346190
    [Abstract] [Full Text] [Related]

  • 7. Electrostatic and non-electrostatic contributions to the binding free energies of anthracycline antibiotics to DNA.
    Baginski M, Fogolari F, Briggs JM.
    J Mol Biol; 1997 Nov 28; 274(2):253-67. PubMed ID: 9398531
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  • 8. A free-energy perturbation method based on Monte Carlo simulations using quantum mechanical calculations (QM/MC/FEP method): application to highly solvent-dependent reactions.
    Hori K, Yamaguchi T, Uezu K, Sumimoto M.
    J Comput Chem; 2011 Apr 15; 32(5):778-86. PubMed ID: 21341291
    [Abstract] [Full Text] [Related]

  • 9. Calculations of solute and solvent entropies from molecular dynamics simulations.
    Carlsson J, Aqvist J.
    Phys Chem Chem Phys; 2006 Dec 14; 8(46):5385-95. PubMed ID: 17119645
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  • 11. Grand canonical free-energy calculations of protein-ligand binding.
    Clark M, Meshkat S, Wiseman JS.
    J Chem Inf Model; 2009 Apr 14; 49(4):934-43. PubMed ID: 19309088
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  • 12. Accurate prediction of protonation state as a prerequisite for reliable MM-PB(GB)SA binding free energy calculations of HIV-1 protease inhibitors.
    Wittayanarakul K, Hannongbua S, Feig M.
    J Comput Chem; 2008 Apr 15; 29(5):673-85. PubMed ID: 17849388
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  • 14. A detailed binding free energy study of 2:1 ligand-DNA complex formation by experiment and simulation.
    Treesuwan W, Wittayanarakul K, Anthony NG, Huchet G, Alniss H, Hannongbua S, Khalaf AI, Suckling CJ, Parkinson JA, Mackay SP.
    Phys Chem Chem Phys; 2009 Dec 07; 11(45):10682-93. PubMed ID: 20145812
    [Abstract] [Full Text] [Related]

  • 15. Application of the lambda-dynamics method to evaluate the relative binding free energies of inhibitors to HCV protease.
    Guo Z, Durkin J, Fischmann T, Ingram R, Prongay A, Zhang R, Madison V.
    J Med Chem; 2003 Dec 04; 46(25):5360-4. PubMed ID: 14640544
    [Abstract] [Full Text] [Related]

  • 16. 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
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