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1173 related items for PubMed ID: 28064081

  • 1. 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; 72():70-80. PubMed ID: 28064081
    [Abstract] [Full Text] [Related]

  • 2. 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
    [Abstract] [Full Text] [Related]

  • 3. Protein-Ligand Electrostatic Binding Free Energies from Explicit and Implicit Solvation.
    Izadi S, Aguilar B, Onufriev AV.
    J Chem Theory Comput; 2015 Sep 08; 11(9):4450-9. PubMed ID: 26575935
    [Abstract] [Full Text] [Related]

  • 4. 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
    [Abstract] [Full Text] [Related]

  • 5. Generalized Born and Explicit Solvent Models for Free Energy Calculations in Organic Solvents: Cyclodextrin Dimerization.
    Zhang H, Tan T, van der Spoel D.
    J Chem Theory Comput; 2015 Nov 10; 11(11):5103-13. PubMed ID: 26574308
    [Abstract] [Full Text] [Related]

  • 6. Grid-Based Surface Generalized Born Model for Calculation of Electrostatic Binding Free Energies.
    Forouzesh N, Izadi S, Onufriev AV.
    J Chem Inf Model; 2017 Oct 23; 57(10):2505-2513. PubMed ID: 28786669
    [Abstract] [Full Text] [Related]

  • 7. Combining the polarizable Drude force field with a continuum electrostatic Poisson-Boltzmann implicit solvation model.
    Aleksandrov A, Lin FY, Roux B, MacKerell AD.
    J Comput Chem; 2018 Aug 15; 39(22):1707-1719. PubMed ID: 29737546
    [Abstract] [Full Text] [Related]

  • 8. Generalized Born implicit solvent models for small molecule hydration free energies.
    Brieg M, Setzler J, Albert S, Wenzel W.
    Phys Chem Chem Phys; 2017 Jan 04; 19(2):1677-1685. PubMed ID: 27995260
    [Abstract] [Full Text] [Related]

  • 9. Solvation forces on biomolecular structures: a comparison of explicit solvent and Poisson-Boltzmann models.
    Wagoner J, Baker NA.
    J Comput Chem; 2004 Oct 04; 25(13):1623-9. PubMed ID: 15264256
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  • 11. Continuum solvation models in the linear interaction energy method.
    Carlsson J, Andér M, Nervall M, Aqvist J.
    J Phys Chem B; 2006 Jun 22; 110(24):12034-41. PubMed ID: 16800513
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  • 14. 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
    [Abstract] [Full Text] [Related]

  • 15. Use of the FACTS solvation model for protein-ligand docking calculations. Application to EADock.
    Zoete V, Grosdidier A, Cuendet M, Michielin O.
    J Mol Recognit; 2010 Jun 09; 23(5):457-61. PubMed ID: 20101644
    [Abstract] [Full Text] [Related]

  • 16. Electrostatics of ligand binding: parametrization of the generalized Born model and comparison with the Poisson-Boltzmann approach.
    Liu HY, Zou X.
    J Phys Chem B; 2006 May 11; 110(18):9304-13. PubMed ID: 16671749
    [Abstract] [Full Text] [Related]

  • 17. Trypsin-ligand binding free energies from explicit and implicit solvent simulations with polarizable potential.
    Jiao D, Zhang J, Duke RE, Li G, Schnieders MJ, Ren P.
    J Comput Chem; 2009 Aug 11; 30(11):1701-11. PubMed ID: 19399779
    [Abstract] [Full Text] [Related]

  • 18. Comparison of MM/GBSA calculations based on explicit and implicit solvent simulations.
    Godschalk F, Genheden S, Söderhjelm P, Ryde U.
    Phys Chem Chem Phys; 2013 May 28; 15(20):7731-9. PubMed ID: 23595060
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  • 20. 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]

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