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Journal Abstract Search

106 related items for PubMed ID: 19585658

  • 21. Assessing protein kinase selectivity with molecular dynamics and mm-pbsa binding free energy calculations.
    Muzzioli E, Del Rio A, Rastelli G.
    Chem Biol Drug Des; 2011 Aug; 78(2):252-9. PubMed ID: 21585710
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  • 22. Matrix metalloproteinase triple-helical peptidase activities are differentially regulated by substrate stability.
    Minond D, Lauer-Fields JL, Nagase H, Fields GB.
    Biochemistry; 2004 Sep 14; 43(36):11474-81. PubMed ID: 15350133
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  • 23. 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 14; 13(29):8139-52. PubMed ID: 17763506
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  • 24. A molecular basis for the selectivity of thiadiazole urea inhibitors with stromelysin-1 and gelatinase-A from generalized born molecular dynamics simulations.
    Rizzo RC, Toba S, Kuntz ID.
    J Med Chem; 2004 Jun 03; 47(12):3065-74. PubMed ID: 15163188
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  • 25. Cloning, expression and characterisation of Erwinia carotovora L-asparaginase.
    Kotzia GA, Labrou NE.
    J Biotechnol; 2005 Oct 10; 119(4):309-23. PubMed ID: 15951039
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  • 26. Improving the interaction of Myc-interfering peptides with Myc using molecular dynamics simulations.
    Jouaux EM, Timm BB, Arndt KM, Exner TE.
    J Pept Sci; 2009 Jan 10; 15(1):5-15. PubMed ID: 19035580
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  • 27. Characterization by NMR and molecular modeling of the binding of polyisoprenols and polyisoprenyl recognition sequence peptides: 3D structure of the complexes reveals sites of specific interactions.
    Zhou GP, Troy FA.
    Glycobiology; 2003 Feb 10; 13(2):51-71. PubMed ID: 12626407
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  • 28. The reaction mechanism of paraoxon hydrolysis by phosphotriesterase from combined QM/MM simulations.
    Wong KY, Gao J.
    Biochemistry; 2007 Nov 20; 46(46):13352-69. PubMed ID: 17966992
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  • 29. Comparative molecular dynamics simulations of histone deacetylase-like protein: binding modes and free energy analysis to hydroxamic acid inhibitors.
    Yan C, Xiu Z, Li X, Li S, Hao C, Teng H.
    Proteins; 2008 Oct 20; 73(1):134-49. PubMed ID: 18398905
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  • 30. Validation of an automated procedure for the prediction of relative free energies of binding on a set of aldose reductase inhibitors.
    Ferrari AM, Degliesposti G, Sgobba M, Rastelli G.
    Bioorg Med Chem; 2007 Dec 15; 15(24):7865-77. PubMed ID: 17870536
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  • 31. Synthesis and evaluation of new tripeptide phosphonate inhibitors of MMP-8 and MMP-2.
    Agamennone M, Campestre C, Preziuso S, Consalvi V, Crucianelli M, Mazza F, Politi V, Ragno R, Tortorella P, Gallina C.
    Eur J Med Chem; 2005 Mar 15; 40(3):271-9. PubMed ID: 15725496
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  • 32. 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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  • 33. Molecular dynamics simulations of human LRH-1: the impact of ligand binding in a constitutively active nuclear receptor.
    Burendahl S, Treuter E, Nilsson L.
    Biochemistry; 2008 May 06; 47(18):5205-15. PubMed ID: 18410128
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  • 34. An integrated computational and experimental approach to gaining selectivity for MMP-2 within the gelatinase subfamily.
    Fabre B, Filipiak K, Díaz N, Zapico JM, Suárez D, Ramos A, de Pascual-Teresa B.
    Chembiochem; 2014 Feb 10; 15(3):399-412. PubMed ID: 24449516
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  • 35. Mechanistic role of an NS4A peptide cofactor with the truncated NS3 protease of hepatitis C virus: elucidation of the NS4A stimulatory effect via kinetic analysis and inhibitor mapping.
    Landro JA, Raybuck SA, Luong YP, O'Malley ET, Harbeson SL, Morgenstern KA, Rao G, Livingston DJ.
    Biochemistry; 1997 Aug 05; 36(31):9340-8. PubMed ID: 9235976
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  • 36. Comparison between computational alanine scanning and per-residue binding free energy decomposition for protein-protein association using MM-GBSA: application to the TCR-p-MHC complex.
    Zoete V, Michielin O.
    Proteins; 2007 Jun 01; 67(4):1026-47. PubMed ID: 17377991
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  • 37. VHR and PTP1 protein phosphatases exhibit remarkably different active site specificities toward low molecular weight nonpeptidic substrates.
    Chen L, Montserat J, Lawrence DS, Zhang ZY.
    Biochemistry; 1996 Jul 23; 35(29):9349-54. PubMed ID: 8755712
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  • 38. Mechanism of proteolysis in matrix metalloproteinase-2 revealed by QM/MM modeling.
    Vasilevskaya T, Khrenova MG, Nemukhin AV, Thiel W.
    J Comput Chem; 2015 Aug 05; 36(21):1621-30. PubMed ID: 26132652
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  • 39. Elucidating the catalytic mechanism of β-secretase (BACE1): a quantum mechanics/molecular mechanics (QM/MM) approach.
    Barman A, Prabhakar R.
    J Mol Graph Model; 2013 Mar 05; 40():1-9. PubMed ID: 23337572
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  • 40. Unraveling the molecular structure of the catalytic domain of matrix metalloproteinase-2 in complex with a triple-helical peptide by means of molecular dynamics simulations.
    Díaz N, Suárez D, Valdés H.
    Biochemistry; 2013 Nov 26; 52(47):8556-69. PubMed ID: 24164447
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