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Journal Abstract Search

385 related items for PubMed ID: 20151411

  • 21. Calculation of absolute ligand binding free energy to a ribosome-targeting protein as a function of solvent model.
    Lee MS, Olson MA.
    J Phys Chem B; 2008 Oct 23; 112(42):13411-7. PubMed ID: 18821791
    [Abstract] [Full Text] [Related]

  • 22. Molecular insight into pseudolysin inhibition using the MM-PBSA and LIE methods.
    Adekoya OA, Willassen NP, Sylte I.
    J Struct Biol; 2006 Feb 23; 153(2):129-44. PubMed ID: 16376106
    [Abstract] [Full Text] [Related]

  • 23. 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
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  • 24. Exploring the conformational changes of the ATP binding site of gyrase B from Escherichia coli complexed with different established inhibitors by using molecular dynamics simulation: protein-ligand interactions in the light of the alanine scanning and free energy decomposition methods.
    Saíz-Urra L, Cabrera MA, Froeyen M.
    J Mol Graph Model; 2011 Feb 15; 29(5):726-39. PubMed ID: 21216167
    [Abstract] [Full Text] [Related]

  • 25. Free energies of binding of polychlorinated biphenyls to the estrogen receptor from a single simulation.
    Oostenbrink C, van Gunsteren WF.
    Proteins; 2004 Feb 01; 54(2):237-46. PubMed ID: 14696186
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  • 26. 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
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  • 28. 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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  • 31. Analyses of activity for factor Xa inhibitors based on Monte Carlo simulations.
    Ostrovsky D, Udier-Blagović M, Jorgensen WL.
    J Med Chem; 2003 Dec 18; 46(26):5691-9. PubMed ID: 14667222
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  • 32. pKa calculations in solution and proteins with QM/MM free energy perturbation simulations: a quantitative test of QM/MM protocols.
    Riccardi D, Schaefer P, Cui Q.
    J Phys Chem B; 2005 Sep 22; 109(37):17715-33. PubMed ID: 16853267
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  • 34. Calculation of absolute protein-ligand binding constants with the molecular dynamics free energy perturbation method.
    Woo HJ.
    Methods Mol Biol; 2008 Sep 22; 443():109-20. PubMed ID: 18446284
    [Abstract] [Full Text] [Related]

  • 35. 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
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  • 37. New parameterization approaches of the LIE method to improve free energy calculations of PlmII-Inhibitors complexes.
    Valiente PA, Gil A, Batista PR, Caffarena ER, Pons T, Pascutti PG.
    J Comput Chem; 2010 Nov 30; 31(15):2723-34. PubMed ID: 20839299
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  • 38. Molecular insights into 14-membered macrolides using the MM-PBSA method.
    Yam WK, Wahab HA.
    J Chem Inf Model; 2009 Jun 30; 49(6):1558-67. PubMed ID: 19469526
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  • 40. Structure and thermodynamics of RNA-protein binding: using molecular dynamics and free energy analyses to calculate the free energies of binding and conformational change.
    Reyes CM, Kollman PA.
    J Mol Biol; 2000 Apr 14; 297(5):1145-58. PubMed ID: 10764579
    [Abstract] [Full Text] [Related]

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