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1068 related items for PubMed ID: 23841453

  • 1. Free energies of binding from large-scale first-principles quantum mechanical calculations: application to ligand hydration energies.
    Fox SJ, Pittock C, Tautermann CS, Fox T, Christ C, Malcolm NO, Essex JW, Skylaris CK.
    J Phys Chem B; 2013 Aug 15; 117(32):9478-85. PubMed ID: 23841453
    [Abstract] [Full Text] [Related]

  • 2. A simple QM/MM approach for capturing polarization effects in protein-ligand binding free energy calculations.
    Beierlein FR, Michel J, Essex JW.
    J Phys Chem B; 2011 May 05; 115(17):4911-26. PubMed ID: 21476567
    [Abstract] [Full Text] [Related]

  • 3. Hybrid density functional-molecular mechanics calculations for core-electron binding energies of glycine in water solution.
    Niskanen J, Arul Murugan N, Rinkevicius Z, Vahtras O, Li C, Monti S, Carravetta V, Agren H.
    Phys Chem Chem Phys; 2013 Jan 07; 15(1):244-54. PubMed ID: 23160171
    [Abstract] [Full Text] [Related]

  • 4. Reaction path potential for complex systems derived from combined ab initio quantum mechanical and molecular mechanical calculations.
    Lu Z, Yang W.
    J Chem Phys; 2004 Jul 01; 121(1):89-100. PubMed ID: 15260525
    [Abstract] [Full Text] [Related]

  • 5. A "Stepping Stone" Approach for Obtaining Quantum Free Energies of Hydration.
    Sampson C, Fox T, Tautermann CS, Woods C, Skylaris CK.
    J Phys Chem B; 2015 Jun 11; 119(23):7030-40. PubMed ID: 25985723
    [Abstract] [Full Text] [Related]

  • 6. Computation of Hydration Free Energies Using the Multiple Environment Single System Quantum Mechanical/Molecular Mechanical Method.
    König G, Mei Y, Pickard FC, Simmonett AC, Miller BT, Herbert JM, Woodcock HL, Brooks BR, Shao Y.
    J Chem Theory Comput; 2016 Jan 12; 12(1):332-44. PubMed ID: 26613419
    [Abstract] [Full Text] [Related]

  • 7. Density functional theory calculations on entire proteins for free energies of binding: application to a model polar binding site.
    Fox SJ, Dziedzic J, Fox T, Tautermann CS, Skylaris CK.
    Proteins; 2014 Dec 12; 82(12):3335-46. PubMed ID: 25212393
    [Abstract] [Full Text] [Related]

  • 8. Electrostatic embedding in large-scale first principles quantum mechanical calculations on biomolecules.
    Fox SJ, Pittock C, Fox T, Tautermann CS, Malcolm N, Skylaris CK.
    J Chem Phys; 2011 Dec 14; 135(22):224107. PubMed ID: 22168680
    [Abstract] [Full Text] [Related]

  • 9. Combining ab initio quantum mechanics with a dipole-field model to describe acid dissociation reactions in water: first-principles free energy and entropy calculations.
    Maurer P, Iftimie R.
    J Chem Phys; 2010 Feb 21; 132(7):074112. PubMed ID: 20170220
    [Abstract] [Full Text] [Related]

  • 10. Comparison of charge models for fixed-charge force fields: small-molecule hydration free energies in explicit solvent.
    Mobley DL, Dumont E, Chodera JD, Dill KA.
    J Phys Chem B; 2007 Mar 08; 111(9):2242-54. PubMed ID: 17291029
    [Abstract] [Full Text] [Related]

  • 11. Theoretical modeling of large molecular systems. Advances in the local self consistent field method for mixed quantum mechanics/molecular mechanics calculations.
    Monari A, Rivail JL, Assfeld X.
    Acc Chem Res; 2013 Feb 19; 46(2):596-603. PubMed ID: 23249409
    [Abstract] [Full Text] [Related]

  • 12. Variational calculation of quantum mechanical/molecular mechanical free energy with electronic polarization of solvent.
    Nakano H, Yamamoto T.
    J Chem Phys; 2012 Apr 07; 136(13):134107. PubMed ID: 22482540
    [Abstract] [Full Text] [Related]

  • 13. Examining methods for calculations of binding free energies: LRA, LIE, PDLD-LRA, and PDLD/S-LRA calculations of ligands binding to an HIV protease.
    Sham YY, Chu ZT, Tao H, Warshel A.
    Proteins; 2000 Jun 01; 39(4):393-407. PubMed ID: 10813821
    [Abstract] [Full Text] [Related]

  • 14. Computation of the free energy change associated with one-electron reduction of coenzyme immersed in water: a novel approach within the framework of the quantum mechanical/molecular mechanical method combined with the theory of energy representation.
    Takahashi H, Ohno H, Kishi R, Nakano M, Matubayasi N.
    J Chem Phys; 2008 Nov 28; 129(20):205103. PubMed ID: 19045881
    [Abstract] [Full Text] [Related]

  • 15. Use of a QM/MM-based FEP method to evaluate the anomalous hydration behavior of simple alkyl amines and amides: application to the design of FBPase inhibitors for the treatment of type-2 diabetes.
    Reddy MR, Singh UC, Erion MD.
    J Am Chem Soc; 2011 Jun 01; 133(21):8059-61. PubMed ID: 21545145
    [Abstract] [Full Text] [Related]

  • 16. Quantum mechanics/molecular mechanics minimum free-energy path for accurate reaction energetics in solution and enzymes: sequential sampling and optimization on the potential of mean force surface.
    Hu H, Lu Z, Parks JM, Burger SK, Yang W.
    J Chem Phys; 2008 Jan 21; 128(3):034105. PubMed ID: 18205486
    [Abstract] [Full Text] [Related]

  • 17. Ligand-Binding Affinity Estimates Supported by Quantum-Mechanical Methods.
    Ryde U, Söderhjelm P.
    Chem Rev; 2016 May 11; 116(9):5520-66. PubMed ID: 27077817
    [Abstract] [Full Text] [Related]

  • 18. Quantum mechanics/molecular mechanics modeling of photoelectron spectra: the carbon 1s core-electron binding energies of ethanol-water solutions.
    Löytynoja T, Niskanen J, Jänkälä K, Vahtras O, Rinkevicius Z, Ågren H.
    J Phys Chem B; 2014 Nov 20; 118(46):13217-25. PubMed ID: 25340948
    [Abstract] [Full Text] [Related]

  • 19. Binding affinities by alchemical perturbation using QM/MM with a large QM system and polarizable MM model.
    Genheden S, Ryde U, Söderhjelm P.
    J Comput Chem; 2015 Oct 30; 36(28):2114-24. PubMed ID: 26280564
    [Abstract] [Full Text] [Related]

  • 20. Proceedings of the Second Workshop on Theory meets Industry (Erwin-Schrödinger-Institute (ESI), Vienna, Austria, 12-14 June 2007).
    Hafner J.
    J Phys Condens Matter; 2008 Feb 13; 20(6):060301. PubMed ID: 21693862
    [Abstract] [Full Text] [Related]

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