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Journal Abstract Search

261 related items for PubMed ID: 19399779

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  • 2. Calculation of protein-ligand binding free energy by using a polarizable potential.
    Jiao D, Golubkov PA, Darden TA, Ren P.
    Proc Natl Acad Sci U S A; 2008 Apr 29; 105(17):6290-5. PubMed ID: 18427113
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  • 4. Accuracy comparison of several common implicit solvent models and their implementations in the context of protein-ligand binding.
    Katkova EV, Onufriev AV, Aguilar B, Sulimov VB.
    J Mol Graph Model; 2017 Mar 29; 72():70-80. PubMed ID: 28064081
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  • 8. Non-Boltzmann thermodynamic integration (NBTI) for macromolecular systems: relative free energy of binding of trypsin to benzamidine and benzylamine.
    Ota N, Stroupe C, Ferreira-da-Silva JM, Shah SA, Mares-Guia M, Brunger AT.
    Proteins; 1999 Dec 01; 37(4):641-53. PubMed ID: 10651279
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  • 11. Calculating the binding free energies of charged species based on explicit-solvent simulations employing lattice-sum methods: an accurate correction scheme for electrostatic finite-size effects.
    Rocklin GJ, Mobley DL, Dill KA, Hünenberger PH.
    J Chem Phys; 2013 Nov 14; 139(18):184103. PubMed ID: 24320250
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  • 12. 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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  • 13. Intriguing role of water in protein-ligand binding studied by neutron crystallography on trypsin complexes.
    Schiebel J, Gaspari R, Wulsdorf T, Ngo K, Sohn C, Schrader TE, Cavalli A, Ostermann A, Heine A, Klebe G.
    Nat Commun; 2018 Sep 03; 9(1):3559. PubMed ID: 30177695
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  • 14. Modeling loop reorganization free energies of acetylcholinesterase: a comparison of explicit and implicit solvent models.
    Olson MA.
    Proteins; 2004 Dec 01; 57(4):645-50. PubMed ID: 15481087
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  • 16. Connecting free energy surfaces in implicit and explicit solvent: an efficient method to compute conformational and solvation free energies.
    Deng N, Zhang BW, Levy RM.
    J Chem Theory Comput; 2015 Jun 09; 11(6):2868-78. PubMed ID: 26236174
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  • 17. Quantitative analysis of Poisson-Boltzmann implicit solvent in molecular dynamics.
    Wang J, Tan C, Chanco E, Luo R.
    Phys Chem Chem Phys; 2010 Feb 07; 12(5):1194-202. PubMed ID: 20094685
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  • 19. Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations.
    Buch I, Giorgino T, De Fabritiis G.
    Proc Natl Acad Sci U S A; 2011 Jun 21; 108(25):10184-9. PubMed ID: 21646537
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  • 20. Evaluation of protein-protein docking model structures using all-atom molecular dynamics simulations combined with the solution theory in the energy representation.
    Takemura K, Guo H, Sakuraba S, Matubayasi N, Kitao A.
    J Chem Phys; 2012 Dec 07; 137(21):215105. PubMed ID: 23231264
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