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1118 related items for PubMed ID: 8346190

  • 1. 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; 16(3):226-45. PubMed ID: 8346190
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  • 2. 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
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  • 3. Electronic structure, binding energy, and solvation structure of the streptavidin-biotin supramolecular complex: ONIOM and 3D-RISM study.
    Li Q, Gusarov S, Evoy S, Kovalenko A.
    J Phys Chem B; 2009 Jul 23; 113(29):9958-67. PubMed ID: 19545155
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  • 4. Energetic roles of hydrogen bonds at the ureido oxygen binding pocket in the streptavidin-biotin complex.
    Klumb LA, Chu V, Stayton PS.
    Biochemistry; 1998 May 26; 37(21):7657-63. PubMed ID: 9601024
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  • 5. Calculation of the relative binding free energy of 2'GMP and 2'AMP to ribonuclease T1 using molecular dynamics/free energy perturbation approaches.
    Hirono S, Kollman PA.
    J Mol Biol; 1990 Mar 05; 212(1):197-209. PubMed ID: 2157020
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  • 6. 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
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  • 7. 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
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  • 10. Free energy simulations and MM-PBSA analyses on the affinity and specificity of steroid binding to antiestradiol antibody.
    Laitinen T, Kankare JA, Peräkylä M.
    Proteins; 2004 Apr 01; 55(1):34-43. PubMed ID: 14997538
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  • 12. A molecular dynamics study of thermodynamic and structural aspects of the hydration of cavities in proteins.
    Wade RC, Mazor MH, McCammon JA, Quiocho FA.
    Biopolymers; 1991 Jul 01; 31(8):919-31. PubMed ID: 1782354
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  • 13. 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
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  • 19. 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
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