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385 related items for PubMed ID: 20151411

  • 1. 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; 23(2):128-41. PubMed ID: 20151411
    [Abstract] [Full Text] [Related]

  • 2. 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]

  • 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
    [Abstract] [Full Text] [Related]

  • 5. 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]

  • 6. Prediction of ligand binding affinity and orientation of xenoestrogens to the estrogen receptor by molecular dynamics simulations and the linear interaction energy method.
    van Lipzig MM, ter Laak AM, Jongejan A, Vermeulen NP, Wamelink M, Geerke D, Meerman JH.
    J Med Chem; 2004 Feb 12; 47(4):1018-30. PubMed ID: 14761204
    [Abstract] [Full Text] [Related]

  • 7. Calculation of Standard Binding Free Energies:  Aromatic Molecules in the T4 Lysozyme L99A Mutant.
    Deng Y, Roux B.
    J Chem Theory Comput; 2006 Sep 12; 2(5):1255-73. PubMed ID: 26626834
    [Abstract] [Full Text] [Related]

  • 8. Exhaustive mutagenesis in silico: multicoordinate free energy calculations on proteins and peptides.
    Pitera JW, Kollman PA.
    Proteins; 2000 Nov 15; 41(3):385-97. PubMed ID: 11025549
    [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 15; 49(4):934-43. PubMed ID: 19309088
    [Abstract] [Full Text] [Related]

  • 10. Grand canonical Monte Carlo simulation of ligand-protein binding.
    Clark M, Guarnieri F, Shkurko I, Wiseman J.
    J Chem Inf Model; 2006 Apr 15; 46(1):231-42. PubMed ID: 16426059
    [Abstract] [Full Text] [Related]

  • 11. Prediction of the binding free energies of new TIBO-like HIV-1 reverse transcriptase inhibitors using a combination of PROFEC, PB/SA, CMC/MD, and free energy calculations.
    Eriksson MA, Pitera J, Kollman PA.
    J Med Chem; 1999 Mar 11; 42(5):868-81. PubMed ID: 10072684
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  • 13. What determines the van der Waals coefficient beta in the LIE (linear interaction energy) method to estimate binding free energies using molecular dynamics simulations?
    Wang W, Wang J, Kollman PA.
    Proteins; 1999 Feb 15; 34(3):395-402. PubMed ID: 10024025
    [Abstract] [Full Text] [Related]

  • 14. 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]

  • 15. Molecular recognition of RNA: challenges for modelling interactions and plasticity.
    Fulle S, Gohlke H.
    J Mol Recognit; 2010 Feb 07; 23(2):220-31. PubMed ID: 19941322
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  • 18. 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 07; 26(12):1294-305. PubMed ID: 15981257
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