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Journal Abstract Search

250 related items for PubMed ID: 10450088

  • 21. Structural analysis of lead fullerene-based inhibitor bound to human immunodeficiency virus type 1 protease in solution from molecular dynamics simulations.
    Lee VS, Nimmanpipug P, Aruksakunwong O, Promsri S, Sompornpisut P, Hannongbua S.
    J Mol Graph Model; 2007 Sep; 26(2):558-70. PubMed ID: 17468026
    [Abstract] [Full Text] [Related]

  • 22. Inhibitor binding at the protein interface in crystals of a HIV-1 protease complex.
    Brynda J, Rezácová P, Fábry M, Horejsí M, Stouracová R, Soucek M, Hradílek M, Konvalinka J, Sedlácek J.
    Acta Crystallogr D Biol Crystallogr; 2004 Nov; 60(Pt 11):1943-8. PubMed ID: 15502300
    [Abstract] [Full Text] [Related]

  • 23. Structure-based QSAR analysis of a set of 4-hydroxy-5,6-dihydropyrones as inhibitors of HIV-1 protease: an application of the receptor-dependent (RD) 4D-QSAR formalism.
    Santos-Filho OA, Hopfinger AJ.
    J Chem Inf Model; 2006 Nov; 46(1):345-54. PubMed ID: 16426069
    [Abstract] [Full Text] [Related]

  • 24. MCSS functionality maps for a flexible protein.
    Stultz CM, Karplus M.
    Proteins; 1999 Dec 01; 37(4):512-29. PubMed ID: 10651268
    [Abstract] [Full Text] [Related]

  • 25. Structure, dynamics and solvation of HIV-1 protease/saquinavir complex in aqueous solution and their contributions to drug resistance: molecular dynamic simulations.
    Wittayanarakul K, Aruksakunwong O, Sompornpisut P, Sanghiran-Lee V, Parasuk V, Pinitglang S, Hannongbua S.
    J Chem Inf Model; 2005 Dec 01; 45(2):300-8. PubMed ID: 15807491
    [Abstract] [Full Text] [Related]

  • 26. The effect of inhibitor binding on the structural stability and cooperativity of the HIV-1 protease.
    Todd MJ, Freire E.
    Proteins; 1999 Aug 01; 36(2):147-56. PubMed ID: 10398363
    [Abstract] [Full Text] [Related]

  • 27. FDS: flexible ligand and receptor docking with a continuum solvent model and soft-core energy function.
    Taylor RD, Jewsbury PJ, Essex JW.
    J Comput Chem; 2003 Oct 01; 24(13):1637-56. PubMed ID: 12926007
    [Abstract] [Full Text] [Related]

  • 28. A major role for a set of non-active site mutations in the development of HIV-1 protease drug resistance.
    Muzammil S, Ross P, Freire E.
    Biochemistry; 2003 Jan 28; 42(3):631-8. PubMed ID: 12534275
    [Abstract] [Full Text] [Related]

  • 29. Comparative binding energy analysis of HIV-1 protease inhibitors: incorporation of solvent effects and validation as a powerful tool in receptor-based drug design.
    Pérez C, Pastor M, Ortiz AR, Gago F.
    J Med Chem; 1998 Mar 12; 41(6):836-52. PubMed ID: 9526559
    [Abstract] [Full Text] [Related]

  • 30. Empirical free energy calculations of human immunodeficiency virus type 1 protease crystallographic complexes. II. Knowledge-based ligand-protein interaction potentials applied to thermodynamic analysis of hydrophobic mutations.
    Verkhivker GM.
    Pac Symp Biocomput; 1996 Mar 12; ():638-52. PubMed ID: 9390264
    [Abstract] [Full Text] [Related]

  • 31. Molecular dynamics study of the connection between flap closing and binding of fullerene-based inhibitors of the HIV-1 protease.
    Zhu Z, Schuster DI, Tuckerman ME.
    Biochemistry; 2003 Feb 11; 42(5):1326-33. PubMed ID: 12564936
    [Abstract] [Full Text] [Related]

  • 32. 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
    [Abstract] [Full Text] [Related]

  • 33. Structure-based ligand design for flexible proteins: application of new F-DycoBlock.
    Zhu J, Fan H, Liu H, Shi Y.
    J Comput Aided Mol Des; 2001 Nov 15; 15(11):979-96. PubMed ID: 11989626
    [Abstract] [Full Text] [Related]

  • 34. Design, synthesis, evaluation, and crystallographic-based structural studies of HIV-1 protease inhibitors with reduced response to the V82A mutation.
    Clemente JC, Robbins A, Graña P, Paleo MR, Correa JF, Villaverde MC, Sardina FJ, Govindasamy L, Agbandje-McKenna M, McKenna R, Dunn BM, Sussman F.
    J Med Chem; 2008 Feb 28; 51(4):852-60. PubMed ID: 18215016
    [Abstract] [Full Text] [Related]

  • 35. Molecular basis of resistance to HIV-1 protease inhibition: a plausible hypothesis.
    Luque I, Todd MJ, Gómez J, Semo N, Freire E.
    Biochemistry; 1998 Apr 28; 37(17):5791-7. PubMed ID: 9558312
    [Abstract] [Full Text] [Related]

  • 36. A hybrid method of molecular dynamics and harmonic dynamics for docking of flexible ligand to flexible receptor.
    Tatsumi R, Fukunishi Y, Nakamura H.
    J Comput Chem; 2004 Dec 28; 25(16):1995-2005. PubMed ID: 15473011
    [Abstract] [Full Text] [Related]

  • 37. Improving binding mode predictions by docking into protein-specifically adapted potential fields.
    Radestock S, Böhm M, Gohlke H.
    J Med Chem; 2005 Aug 25; 48(17):5466-79. PubMed ID: 16107145
    [Abstract] [Full Text] [Related]

  • 38. Rapid and accurate prediction of binding free energies for saquinavir-bound HIV-1 proteases.
    Stoica I, Sadiq SK, Coveney PV.
    J Am Chem Soc; 2008 Feb 27; 130(8):2639-48. PubMed ID: 18225901
    [Abstract] [Full Text] [Related]

  • 39. E-novo: an automated workflow for efficient structure-based lead optimization.
    Pearce BC, Langley DR, Kang J, Huang H, Kulkarni A.
    J Chem Inf Model; 2009 Jul 27; 49(7):1797-809. PubMed ID: 19552372
    [Abstract] [Full Text] [Related]

  • 40.
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