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Journal Abstract Search

329 related items for PubMed ID: 17335007

  • 21. Computational identification of self-inhibitory peptides from envelope proteins.
    Xu Y, Rahman NA, Othman R, Hu P, Huang M.
    Proteins; 2012 Aug; 80(9):2154-68. PubMed ID: 22544824
    [Abstract] [Full Text] [Related]

  • 22. An optimized MM/PBSA virtual screening approach applied to an HIV-1 gp41 fusion peptide inhibitor.
    Venken T, Krnavek D, Münch J, Kirchhoff F, Henklein P, De Maeyer M, Voet A.
    Proteins; 2011 Nov; 79(11):3221-35. PubMed ID: 21989940
    [Abstract] [Full Text] [Related]

  • 23. Monte Carlo simulations of the peptide recognition at the consensus binding site of the constant fragment of human immunoglobulin G: the energy landscape analysis of a hot spot at the intermolecular interface.
    Verkhivker GM, Bouzida D, Gehlhaar DK, Rejto PA, Freer ST, Rose PW.
    Proteins; 2002 Aug 15; 48(3):539-57. PubMed ID: 12112677
    [Abstract] [Full Text] [Related]

  • 24. Molecular dynamic investigation of the interaction of supported affinity ligands with monoclonal antibodies.
    Zamolo L, Busini V, Moiani D, Moscatelli D, Cavallotti C.
    Biotechnol Prog; 2008 Aug 15; 24(3):527-39. PubMed ID: 18452341
    [Abstract] [Full Text] [Related]

  • 25. Are solvation free energies of homogeneous helical peptides additive?
    Staritzbichler R, Gu W, Helms V.
    J Phys Chem B; 2005 Oct 13; 109(40):19000-7. PubMed ID: 16853446
    [Abstract] [Full Text] [Related]

  • 26. Origins of resistance to the HIVgp41 viral entry inhibitor T20.
    McGillick BE, Balius TE, Mukherjee S, Rizzo RC.
    Biochemistry; 2010 May 04; 49(17):3575-92. PubMed ID: 20230061
    [Abstract] [Full Text] [Related]

  • 27. X-ray crystallographic study of an HIV-1 fusion inhibitor with the gp41 S138A substitution.
    Watabe T, Terakawa Y, Watanabe K, Ohno H, Nakano H, Nakatsu T, Kato H, Izumi K, Kodama E, Matsuoka M, Kitaura K, Oishi S, Fujii N.
    J Mol Biol; 2009 Sep 25; 392(3):657-65. PubMed ID: 19616557
    [Abstract] [Full Text] [Related]

  • 28. Computational modeling and surface plasmon resonance analyses in the assessment of peptide ligands interacting with fibrin gamma(312-324) epitope.
    Massarelli I, Bianucci AM, Chiellini F, Eidelman C, Chiellini E.
    Eur J Med Chem; 2009 May 25; 44(5):2128-34. PubMed ID: 19058882
    [Abstract] [Full Text] [Related]

  • 29. Incorporating receptor flexibility in the molecular design of protein interfaces.
    Li L, Liang S, Pilcher MM, Meroueh SO.
    Protein Eng Des Sel; 2009 Sep 25; 22(9):575-86. PubMed ID: 19643976
    [Abstract] [Full Text] [Related]

  • 30. Force-field development and molecular dynamics simulations of ferrocene-peptide conjugates as a scaffold for hydrogenase mimics.
    de Hatten X, Cournia Z, Huc I, Smith JC, Metzler-Nolte N.
    Chemistry; 2007 Sep 25; 13(29):8139-52. PubMed ID: 17763506
    [Abstract] [Full Text] [Related]

  • 31. Predicting peptide binding to MHC pockets via molecular modeling, implicit solvation, and global optimization.
    Schafroth HD, Floudas CA.
    Proteins; 2004 Feb 15; 54(3):534-56. PubMed ID: 14748001
    [Abstract] [Full Text] [Related]

  • 32. Molecular dynamics-solvated interaction energy studies of protein-protein interactions: the MP1-p14 scaffolding complex.
    Cui Q, Sulea T, Schrag JD, Munger C, Hung MN, Naïm M, Cygler M, Purisima EO.
    J Mol Biol; 2008 Jun 13; 379(4):787-802. PubMed ID: 18479705
    [Abstract] [Full Text] [Related]

  • 33. Bridge water mediates nevirapine binding to wild type and Y181C HIV-1 reverse transcriptase--evidence from molecular dynamics simulations and MM-PBSA calculations.
    Treesuwan W, Hannongbua S.
    J Mol Graph Model; 2009 Jun 13; 27(8):921-9. PubMed ID: 19414275
    [Abstract] [Full Text] [Related]

  • 34. Solvation free energies of amino acid side chain analogs for common molecular mechanics water models.
    Shirts MR, Pande VS.
    J Chem Phys; 2005 Apr 01; 122(13):134508. PubMed ID: 15847482
    [Abstract] [Full Text] [Related]

  • 35. How inaccuracies in protein structure models affect estimates of protein-ligand interactions: computational analysis of HIV-I protease inhibitor binding.
    Thorsteinsdottir HB, Schwede T, Zoete V, Meuwly M.
    Proteins; 2006 Nov 01; 65(2):407-23. PubMed ID: 16941468
    [Abstract] [Full Text] [Related]

  • 36. Flexibility of the MHC class II peptide binding cleft in the bound, partially filled, and empty states: a molecular dynamics simulation study.
    Yaneva R, Springer S, Zacharias M.
    Biopolymers; 2009 Jan 01; 91(1):14-27. PubMed ID: 18767126
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  • 37. Scoring binding affinity of multiple ligands using implicit solvent and a single molecular dynamics trajectory: application to influenza neuraminidase.
    Bonnet P, Bryce RA.
    J Mol Graph Model; 2005 Oct 01; 24(2):147-56. PubMed ID: 16098779
    [Abstract] [Full Text] [Related]

  • 38. FURSMASA: a new approach to rapid scoring functions that uses a MD-averaged potential energy grid and a solvent-accessible surface area term with parameters GA fit to experimental data.
    Pearlman DA, Rao BG, Charifson P.
    Proteins; 2008 May 15; 71(3):1519-38. PubMed ID: 18300249
    [Abstract] [Full Text] [Related]

  • 39. Automated molecular simulation based binding affinity calculator for ligand-bound HIV-1 proteases.
    Sadiq SK, Wright D, Watson SJ, Zasada SJ, Stoica I, Coveney PV.
    J Chem Inf Model; 2008 Sep 15; 48(9):1909-19. PubMed ID: 18710212
    [Abstract] [Full Text] [Related]

  • 40. Cutoff size need not strongly influence molecular dynamics results for solvated polypeptides.
    Beck DA, Armen RS, Daggett V.
    Biochemistry; 2005 Jan 18; 44(2):609-16. PubMed ID: 15641786
    [Abstract] [Full Text] [Related]

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