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Journal Abstract Search

209 related items for PubMed ID: 20099932

  • 41. Continuum solvent studies of the stability of RNA hairpin loops and helices.
    Srinivasan J, Miller J, Kollman PA, Case DA.
    J Biomol Struct Dyn; 1998 Dec; 16(3):671-82. PubMed ID: 10052623
    [Abstract] [Full Text] [Related]

  • 42. Calculation of ligand-nucleic acid binding free energies with the generalized-born model in DOCK.
    Kang X, Shafer RH, Kuntz ID.
    Biopolymers; 2004 Feb 05; 73(2):192-204. PubMed ID: 14755577
    [Abstract] [Full Text] [Related]

  • 43. Including explicit water molecules as part of the protein structure in MM/PBSA calculations.
    Zhu YL, Beroza P, Artis DR.
    J Chem Inf Model; 2014 Feb 24; 54(2):462-9. PubMed ID: 24432790
    [Abstract] [Full Text] [Related]

  • 44. Alchemical free energy calculations via metadynamics: Application to the theophylline-RNA aptamer complex.
    Tanida Y, Matsuura A.
    J Comput Chem; 2020 Jul 30; 41(20):1804-1819. PubMed ID: 32449538
    [Abstract] [Full Text] [Related]

  • 45. Addressing limitations with the MM-GB/SA scoring procedure using the WaterMap method and free energy perturbation calculations.
    Guimarães CR, Mathiowetz AM.
    J Chem Inf Model; 2010 Apr 26; 50(4):547-59. PubMed ID: 20235592
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  • 46. The treatment of solvation by a generalized Born model and a self-consistent charge-density functional theory-based tight-binding method.
    Xie L, Liu H.
    J Comput Chem; 2002 Nov 30; 23(15):1404-15. PubMed ID: 12370943
    [Abstract] [Full Text] [Related]

  • 47. Validation and use of the MM-PBSA approach for drug discovery.
    Kuhn B, Gerber P, Schulz-Gasch T, Stahl M.
    J Med Chem; 2005 Jun 16; 48(12):4040-8. PubMed ID: 15943477
    [Abstract] [Full Text] [Related]

  • 48. Solvated interaction energy (SIE) for scoring protein-ligand binding affinities. 1. Exploring the parameter space.
    Naïm M, Bhat S, Rankin KN, Dennis S, Chowdhury SF, Siddiqi I, Drabik P, Sulea T, Bayly CI, Jakalian A, Purisima EO.
    J Chem Inf Model; 2007 Jun 16; 47(1):122-33. PubMed ID: 17238257
    [Abstract] [Full Text] [Related]

  • 49. Discrimination between native and intentionally misfolded conformations of proteins: ES/IS, a new method for calculating conformational free energy that uses both dynamics simulations with an explicit solvent and an implicit solvent continuum model.
    Vorobjev YN, Almagro JC, Hermans J.
    Proteins; 1998 Sep 01; 32(4):399-413. PubMed ID: 9726412
    [Abstract] [Full Text] [Related]

  • 50. Molecular basis of the interaction for an essential subunit PA-PB1 in influenza virus RNA polymerase: insights from molecular dynamics simulation and free energy calculation.
    Liu H, Yao X.
    Mol Pharm; 2010 Feb 01; 7(1):75-85. PubMed ID: 19883112
    [Abstract] [Full Text] [Related]

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  • 52. Electrostatic solvation free energy of amino acid side chain analogs: implications for the validity of electrostatic linear response in water.
    Lin B, Pettitt BM.
    J Comput Chem; 2011 Apr 15; 32(5):878-85. PubMed ID: 20941733
    [Abstract] [Full Text] [Related]

  • 53. Molecular dynamics investigation on a series of HIV protease inhibitors: assessing the performance of MM-PBSA and MM-GBSA approaches.
    Srivastava HK, Sastry GN.
    J Chem Inf Model; 2012 Nov 26; 52(11):3088-98. PubMed ID: 23121465
    [Abstract] [Full Text] [Related]

  • 54. 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
    [Abstract] [Full Text] [Related]

  • 55. A morphometric approach for the accurate solvation thermodynamics of proteins and ligands.
    Harano Y, Roth R, Chiba S.
    J Comput Chem; 2013 Sep 05; 34(23):1969-74. PubMed ID: 23775361
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  • 57. Estimating protein-ligand binding free energy: atomic solvation parameters for partition coefficient and solvation free energy calculation.
    Pei J, Wang Q, Zhou J, Lai L.
    Proteins; 2004 Dec 01; 57(4):651-64. PubMed ID: 15390269
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  • 60. Recognition of RNA by amide modified backbone nucleic acids: molecular dynamics simulations of DNA-RNA hybrids in aqueous solution.
    Nina M, Fonné-Pfister R, Beaudegnies R, Chekatt H, Jung PM, Murphy-Kessabi F, De Mesmaeker A, Wendeborn S.
    J Am Chem Soc; 2005 Apr 27; 127(16):6027-38. PubMed ID: 15839703
    [Abstract] [Full Text] [Related]

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