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Journal Abstract Search

649 related items for PubMed ID: 19045232

  • 1. Calculation of absolute protein-ligand binding free energy using distributed replica sampling.
    Rodinger T, Howell PL, Pomès R.
    J Chem Phys; 2008 Oct 21; 129(15):155102. PubMed ID: 19045232
    [Abstract] [Full Text] [Related]

  • 2. Distributed Replica Sampling.
    Rodinger T, Howell PL, Pomès R.
    J Chem Theory Comput; 2006 May 21; 2(3):725-31. PubMed ID: 26626677
    [Abstract] [Full Text] [Related]

  • 3. Fragment-based computation of binding free energies by systematic sampling.
    Clark M, Meshkat S, Talbot GT, Carnevali P, Wiseman JS.
    J Chem Inf Model; 2009 Aug 21; 49(8):1901-13. PubMed ID: 19610599
    [Abstract] [Full Text] [Related]

  • 4. Reduced Free Energy Perturbation/Hamiltonian Replica Exchange Molecular Dynamics Method with Unbiased Alchemical Thermodynamic Axis.
    Jiang W, Thirman J, Jo S, Roux B.
    J Phys Chem B; 2018 Oct 18; 122(41):9435-9442. PubMed ID: 30253098
    [Abstract] [Full Text] [Related]

  • 5. A water-swap reaction coordinate for the calculation of absolute protein-ligand binding free energies.
    Woods CJ, Malaisree M, Hannongbua S, Mulholland AJ.
    J Chem Phys; 2011 Feb 07; 134(5):054114. PubMed ID: 21303099
    [Abstract] [Full Text] [Related]

  • 6. Enhanced sampling of peptide and protein conformations using replica exchange simulations with a peptide backbone biasing-potential.
    Kannan S, Zacharias M.
    Proteins; 2007 Feb 15; 66(3):697-706. PubMed ID: 17120231
    [Abstract] [Full Text] [Related]

  • 7. Modeling protein-small molecule interactions: structure and thermodynamics of noble gases binding in a cavity in mutant phage T4 lysozyme L99A.
    Mann G, Hermans J.
    J Mol Biol; 2000 Sep 29; 302(4):979-89. PubMed ID: 10993736
    [Abstract] [Full Text] [Related]

  • 8. Molecular dynamics of apo-adenylate kinase: a distance replica exchange method for the free energy of conformational fluctuations.
    Lou H, Cukier RI.
    J Phys Chem B; 2006 Nov 30; 110(47):24121-37. PubMed ID: 17125384
    [Abstract] [Full Text] [Related]

  • 9. Dissociation aided and side chain sampling enhanced Hamiltonian replica exchange.
    Mu Y.
    J Chem Phys; 2009 Apr 28; 130(16):164107. PubMed ID: 19405561
    [Abstract] [Full Text] [Related]

  • 10. Synergistic approach to improve "alchemical" free energy calculation in rugged energy surface.
    Min D, Li H, Li G, Bitetti-Putzer R, Yang W.
    J Chem Phys; 2007 Apr 14; 126(14):144109. PubMed ID: 17444703
    [Abstract] [Full Text] [Related]

  • 11. An optimized replica exchange molecular dynamics method.
    Kamberaj H, van der Vaart A.
    J Chem Phys; 2009 Feb 21; 130(7):074906. PubMed ID: 19239315
    [Abstract] [Full Text] [Related]

  • 12. Hamiltonian replica exchange molecular dynamics using soft-core interactions.
    Hritz J, Oostenbrink C.
    J Chem Phys; 2008 Apr 14; 128(14):144121. PubMed ID: 18412437
    [Abstract] [Full Text] [Related]

  • 13. Testing a flexible-receptor docking algorithm in a model binding site.
    Wei BQ, Weaver LH, Ferrari AM, Matthews BW, Shoichet BK.
    J Mol Biol; 2004 Apr 09; 337(5):1161-82. PubMed ID: 15046985
    [Abstract] [Full Text] [Related]

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  • 15. Sampling enhancement for the quantum mechanical potential based molecular dynamics simulations: a general algorithm and its extension for free energy calculation on rugged energy surface.
    Li H, Yang W.
    J Chem Phys; 2007 Mar 21; 126(11):114104. PubMed ID: 17381193
    [Abstract] [Full Text] [Related]

  • 16. Mapping electron paramagnetic resonance spin label conformations by the simulated scaling method.
    Fajer MI, Li H, Yang W, Fajer PG.
    J Am Chem Soc; 2007 Nov 14; 129(45):13840-6. PubMed ID: 17948993
    [Abstract] [Full Text] [Related]

  • 17. Smart resolution replica exchange: an efficient algorithm for exploring complex energy landscapes.
    Liu P, Voth GA.
    J Chem Phys; 2007 Jan 28; 126(4):045106. PubMed ID: 17286516
    [Abstract] [Full Text] [Related]

  • 18. Exhaustive mutagenesis in silico: multicoordinate free energy calculations on proteins and peptides.
    Pitera JW, Kollman PA.
    Proteins; 2000 Nov 15; 41(3):385-97. PubMed ID: 11025549
    [Abstract] [Full Text] [Related]

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