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128 related items for PubMed ID: 22275089

  • 21. Molecular dynamics simulations of CXCL-8 and its interactions with a receptor peptide, heparin fragments, and sulfated linked cyclitols.
    Gandhi NS, Mancera RL.
    J Chem Inf Model; 2011 Feb 28; 51(2):335-58. PubMed ID: 21299226
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  • 22. Calculations of the free energy of interaction of the c-Fos-c-Jun coiled coil: effects of the solvation model and the inclusion of polarization effects.
    Zuo Z, Gandhi NS, Mancera RL.
    J Chem Inf Model; 2010 Dec 27; 50(12):2201-12. PubMed ID: 21090792
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  • 23. A challenging system: free energy prediction for factor Xa.
    Wallnoefer HG, Liedl KR, Fox T.
    J Comput Chem; 2011 Jun 27; 32(8):1743-52. PubMed ID: 21374633
    [Abstract] [Full Text] [Related]

  • 24. Protein-protein recognition and interaction hot spots in an antigen-antibody complex: free energy decomposition identifies "efficient amino acids".
    Lafont V, Schaefer M, Stote RH, Altschuh D, Dejaegere A.
    Proteins; 2007 May 01; 67(2):418-34. PubMed ID: 17256770
    [Abstract] [Full Text] [Related]

  • 25. Energetics of sequence-specific protein-DNA association: computational analysis of integrase Tn916 binding to its target DNA.
    Gorfe AA, Jelesarov I.
    Biochemistry; 2003 Oct 14; 42(40):11568-76. PubMed ID: 14529266
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  • 26. Molecular dynamics simulations of peptides and proteins with a continuum electrostatic model based on screened Coulomb potentials.
    Hassan SA, Mehler EL, Zhang D, Weinstein H.
    Proteins; 2003 Apr 01; 51(1):109-25. PubMed ID: 12596268
    [Abstract] [Full Text] [Related]

  • 27. Calculating proton uptake/release and binding free energy taking into account ionization and conformation changes induced by protein-inhibitor association: application to plasmepsin, cathepsin D and endothiapepsin-pepstatin complexes.
    Alexov E.
    Proteins; 2004 Aug 15; 56(3):572-84. PubMed ID: 15229889
    [Abstract] [Full Text] [Related]

  • 28. Structure and binding determinants of the recombinant kringle-2 domain of human plasminogen to an internal peptide from a group A Streptococcal surface protein.
    Rios-Steiner JL, Schenone M, Mochalkin I, Tulinsky A, Castellino FJ.
    J Mol Biol; 2001 May 11; 308(4):705-19. PubMed ID: 11350170
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  • 29. Free energy calculations of glycosaminoglycan-protein interactions.
    Gandhi NS, Mancera RL.
    Glycobiology; 2009 Oct 11; 19(10):1103-15. PubMed ID: 19643843
    [Abstract] [Full Text] [Related]

  • 30. Interaction identification of Zif268 and TATA(ZF) proteins with GC-/AT-rich DNA sequence: A theoretical study.
    Yang B, Zhu Y, Wang Y, Chen G.
    J Comput Chem; 2011 Feb 11; 32(3):416-28. PubMed ID: 20658568
    [Abstract] [Full Text] [Related]

  • 31. Structural and thermodynamics characters of isolated α-syn12 peptide: long-time temperature replica-exchange molecular dynamics in aqueous solution.
    Cao Z, Liu L, Wu P, Wang J.
    Acta Biochim Biophys Sin (Shanghai); 2011 Mar 11; 43(3):172-80. PubMed ID: 21289072
    [Abstract] [Full Text] [Related]

  • 32. Molecular dynamics simulations of the active matrix metalloproteinase-2: positioning of the N-terminal fragment and binding of a small peptide substrate.
    Díaz N, Suárez D.
    Proteins; 2008 Jul 11; 72(1):50-61. PubMed ID: 18186480
    [Abstract] [Full Text] [Related]

  • 33. 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
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  • 34. Molecular insights into 14-membered macrolides using the MM-PBSA method.
    Yam WK, Wahab HA.
    J Chem Inf Model; 2009 Jun 15; 49(6):1558-67. PubMed ID: 19469526
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  • 35. Vibrational Stark effect spectroscopy at the interface of Ras and Rap1A bound to the Ras binding domain of RalGDS reveals an electrostatic mechanism for protein-protein interaction.
    Stafford AJ, Ensign DL, Webb LJ.
    J Phys Chem B; 2010 Nov 25; 114(46):15331-44. PubMed ID: 20964430
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  • 36. Proteomic tools for the investigation of human hair structural proteins and evidence of weakness sites on hair keratin coil segments.
    Barthélemy NR, Bednarczyk A, Schaeffer-Reiss C, Jullien D, Van Dorsselaer A, Cavusoglu N.
    Anal Biochem; 2012 Feb 01; 421(1):43-55. PubMed ID: 22056946
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  • 37. Recognition of selected monosaccharides by Pseudomonas aeruginosa Lectin II analyzed by molecular dynamics and free energy calculations.
    Mishra NK, Kríz Z, Wimmerová M, Koca J.
    Carbohydr Res; 2010 Jul 02; 345(10):1432-41. PubMed ID: 20546713
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  • 38. Kinetic and binding effects in peptide substrate selectivity of matrix metalloproteinase-2: Molecular dynamics and QM/MM calculations.
    Díaz N, Suárez D, Suárez E.
    Proteins; 2010 Jan 02; 78(1):1-11. PubMed ID: 19585658
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  • 39. 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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  • 40. MM/PBSA analysis of molecular dynamics simulations of bovine beta-lactoglobulin: free energy gradients in conformational transitions?
    Fogolari F, Moroni E, Wojciechowski M, Baginski M, Ragona L, Molinari H.
    Proteins; 2005 Apr 01; 59(1):91-103. PubMed ID: 15690343
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