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265 related items for PubMed ID: 26626834

  • 21. Binding free energies and free energy components from molecular dynamics and Poisson-Boltzmann calculations. Application to amino acid recognition by aspartyl-tRNA synthetase.
    Archontis G, Simonson T, Karplus M.
    J Mol Biol; 2001 Feb 16; 306(2):307-27. PubMed ID: 11237602
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  • 22. Computations of Absolute Solvation Free Energies of Small Molecules Using Explicit and Implicit Solvent Model.
    Shivakumar D, Deng Y, Roux B.
    J Chem Theory Comput; 2009 Apr 14; 5(4):919-30. PubMed ID: 26609601
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  • 23. 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
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  • 24. Accurate predictions of nonpolar solvation free energies require explicit consideration of binding-site hydration.
    Genheden S, Mikulskis P, Hu L, Kongsted J, Söderhjelm P, Ryde U.
    J Am Chem Soc; 2011 Aug 24; 133(33):13081-92. PubMed ID: 21728337
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  • 25. Improving the LIE Method for Binding Free Energy Calculations of Protein-Ligand Complexes.
    Miranda WE, Noskov SY, Valiente PA.
    J Chem Inf Model; 2015 Sep 28; 55(9):1867-77. PubMed ID: 26180998
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  • 33. A free energy calculation study of the effect of H-->F substitution on binding affinity in ligand-antibody interactions.
    Saito M, Okazaki I, Oda M, Fujii I.
    J Comput Chem; 2005 Feb 28; 26(3):272-82. PubMed ID: 15614800
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  • 34. Comparison of Receptor-Ligand Restraint Schemes for Alchemical Absolute Binding Free Energy Calculations.
    Clark F, Robb G, Cole DJ, Michel J.
    J Chem Theory Comput; 2023 Jun 27; 19(12):3686-3704. PubMed ID: 37285579
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  • 35. Atomic resolution mechanism of ligand binding to a solvent inaccessible cavity in T4 lysozyme.
    Mondal J, Ahalawat N, Pandit S, Kay LE, Vallurupalli P.
    PLoS Comput Biol; 2018 May 27; 14(5):e1006180. PubMed ID: 29775455
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  • 36. Host-Guest Relative Binding Affinities at Density-Functional Theory Level from Semiempirical Molecular Dynamics Simulations.
    Wang M, Mei Y, Ryde U.
    J Chem Theory Comput; 2019 Apr 09; 15(4):2659-2671. PubMed ID: 30811192
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  • 40. 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
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