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219 related items for PubMed ID: 20145812

  • 1. 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]

  • 2. 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 07; 16(3):226-45. PubMed ID: 8346190
    [Abstract] [Full Text] [Related]

  • 3. Energetic diversity of DNA minor-groove recognition by small molecules displayed through some model ligand-DNA systems.
    Lah J, Vesnaver G.
    J Mol Biol; 2004 Sep 03; 342(1):73-89. PubMed ID: 15313608
    [Abstract] [Full Text] [Related]

  • 4. A free energy calculation study of the effect of H-->F substitution on binding affinity in ligand-antibody interactions.
    Saito M, Okazaki I, Oda M, Fujii I.
    J Comput Chem; 2005 Feb 03; 26(3):272-82. PubMed ID: 15614800
    [Abstract] [Full Text] [Related]

  • 5. Thermodynamic analysis of binding between mouse major urinary protein-I and the pheromone 2-sec-butyl-4,5-dihydrothiazole.
    Sharrow SD, Novotny MV, Stone MJ.
    Biochemistry; 2003 May 27; 42(20):6302-9. PubMed ID: 12755635
    [Abstract] [Full Text] [Related]

  • 6. The energetics of HMG box interactions with DNA: thermodynamics of the DNA binding of the HMG box from mouse sox-5.
    Privalov PL, Jelesarov I, Read CM, Dragan AI, Crane-Robinson C.
    J Mol Biol; 1999 Dec 10; 294(4):997-1013. PubMed ID: 10588902
    [Abstract] [Full Text] [Related]

  • 7. Specific binding of hoechst 33258 to the d(CGCAAATTTGCG)2 duplex: calorimetric and spectroscopic studies.
    Haq I, Ladbury JE, Chowdhry BZ, Jenkins TC, Chaires JB.
    J Mol Biol; 1997 Aug 15; 271(2):244-57. PubMed ID: 9268656
    [Abstract] [Full Text] [Related]

  • 8. Binding of netropsin to several DNA constructs: evidence for at least two different 1:1 complexes formed from an -AATT-containing ds-DNA construct and a single minor groove binding ligand.
    Freyer MW, Buscaglia R, Cashman D, Hyslop S, Wilson WD, Chaires JB, Lewis EA.
    Biophys Chem; 2007 Mar 15; 126(1-3):186-96. PubMed ID: 16837123
    [Abstract] [Full Text] [Related]

  • 9. The role of backbone motions in ligand binding to the c-Src SH3 domain.
    Wang C, Pawley NH, Nicholson LK.
    J Mol Biol; 2001 Nov 02; 313(4):873-87. PubMed ID: 11697910
    [Abstract] [Full Text] [Related]

  • 10. A molecular thermodynamic view of DNA-drug interactions: a case study of 25 minor-groove binders.
    Shaikh SA, Ahmed SR, Jayaram B.
    Arch Biochem Biophys; 2004 Sep 01; 429(1):81-99. PubMed ID: 15288812
    [Abstract] [Full Text] [Related]

  • 11. 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]

  • 12. 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
    [Abstract] [Full Text] [Related]

  • 13. A computational investigation of allostery in the catabolite activator protein.
    Li L, Uversky VN, Dunker AK, Meroueh SO.
    J Am Chem Soc; 2007 Dec 19; 129(50):15668-76. PubMed ID: 18041838
    [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. Energetics of binding the mammalian high mobility group protein HMGA2 to poly(dA-dT)2 and poly(dA)-poly(dT).
    Cui T, Wei S, Brew K, Leng F.
    J Mol Biol; 2005 Sep 23; 352(3):629-45. PubMed ID: 16109425
    [Abstract] [Full Text] [Related]

  • 16. Van der Waals interactions dominate ligand-protein association in a protein binding site occluded from solvent water.
    Barratt E, Bingham RJ, Warner DJ, Laughton CA, Phillips SE, Homans SW.
    J Am Chem Soc; 2005 Aug 24; 127(33):11827-34. PubMed ID: 16104761
    [Abstract] [Full Text] [Related]

  • 17. Comparative thermodynamics for monomer and dimer sequence-dependent binding of a heterocyclic dication in the DNA minor groove.
    Wang L, Kumar A, Boykin DW, Bailly C, Wilson WD.
    J Mol Biol; 2002 Mar 29; 317(3):361-74. PubMed ID: 11922670
    [Abstract] [Full Text] [Related]

  • 18. 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]

  • 19. A thermodynamic and structural analysis of DNA minor-groove complex formation.
    Mazur S, Tanious FA, Ding D, Kumar A, Boykin DW, Simpson IJ, Neidle S, Wilson WD.
    J Mol Biol; 2000 Jul 07; 300(2):321-37. PubMed ID: 10873468
    [Abstract] [Full Text] [Related]

  • 20. Free energy determinants of secondary structure formation: I. alpha-Helices.
    Yang AS, Honig B.
    J Mol Biol; 1995 Sep 22; 252(3):351-65. PubMed ID: 7563056
    [Abstract] [Full Text] [Related]

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