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Journal Abstract Search

405 related items for PubMed ID: 22168680

  • 21. Estimates of ligand-binding affinities supported by quantum mechanical methods.
    Söderhjelm P, Kongsted J, Genheden S, Ryde U.
    Interdiscip Sci; 2010 Mar; 2(1):21-37. PubMed ID: 20640794
    [Abstract] [Full Text] [Related]

  • 22. Calculation of the free energy of polarization: quantifying the effect of explicitly treating electronic polarization on the transferability of force-field parameters.
    Geerke DP, van Gunsteren WF.
    J Phys Chem B; 2007 Jun 14; 111(23):6425-36. PubMed ID: 17508737
    [Abstract] [Full Text] [Related]

  • 23. Coarse-grained time-dependent density functional simulation of charge transfer in complex systems: application to hole transfer in DNA.
    Kubar T, Elstner M.
    J Phys Chem B; 2010 Sep 02; 114(34):11221-40. PubMed ID: 20687528
    [Abstract] [Full Text] [Related]

  • 24. pKa calculations in solution and proteins with QM/MM free energy perturbation simulations: a quantitative test of QM/MM protocols.
    Riccardi D, Schaefer P, Cui Q.
    J Phys Chem B; 2005 Sep 22; 109(37):17715-33. PubMed ID: 16853267
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  • 25. 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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  • 26. Protein-ligand binding free energies from exhaustive docking.
    Purisima EO, Hogues H.
    J Phys Chem B; 2012 Jun 14; 116(23):6872-9. PubMed ID: 22432509
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  • 27. A polarizable continuum approach for the study of heterogeneous dielectric environments.
    Iozzi MF, Cossi M, Improta R, Rega N, Barone V.
    J Chem Phys; 2006 May 14; 124(18):184103. PubMed ID: 16709093
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  • 28. Quantum Fragment Based ab Initio Molecular Dynamics for Proteins.
    Liu J, Zhu T, Wang X, He X, Zhang JZ.
    J Chem Theory Comput; 2015 Dec 08; 11(12):5897-905. PubMed ID: 26642993
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  • 29. Structure and dynamics of the hydration shells of the Zn(2+) ion from ab initio molecular dynamics and combined ab initio and classical molecular dynamics simulations.
    Cauët E, Bogatko S, Weare JH, Fulton JL, Schenter GK, Bylaska EJ.
    J Chem Phys; 2010 May 21; 132(19):194502. PubMed ID: 20499974
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  • 30. Nonuniform charge scaling (NUCS): a practical approximation of solvent electrostatic screening in proteins.
    Schwarzl SM, Huang D, Smith JC, Fischer S.
    J Comput Chem; 2005 Oct 21; 26(13):1359-71. PubMed ID: 16021598
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  • 31. Comparison of frozen-density embedding and discrete reaction field solvent models for molecular properties.
    Jacob CR, Neugebauer J, Jensen L, Visscher L.
    Phys Chem Chem Phys; 2006 May 28; 8(20):2349-59. PubMed ID: 16710483
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  • 32. 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
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  • 33. Towards an accurate representation of electrostatics in classical force fields: efficient implementation of multipolar interactions in biomolecular simulations.
    Sagui C, Pedersen LG, Darden TA.
    J Chem Phys; 2004 Jan 01; 120(1):73-87. PubMed ID: 15267263
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  • 34. 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
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  • 35. What governs the charge transfer in DNA? The role of DNA conformation and environment.
    Kubar T, Elstner M.
    J Phys Chem B; 2008 Jul 24; 112(29):8788-98. PubMed ID: 18582109
    [Abstract] [Full Text] [Related]

  • 36. Averaged Solvent Embedding Potential Parameters for Multiscale Modeling of Molecular Properties.
    Beerepoot MT, Steindal AH, List NH, Kongsted J, Olsen JM.
    J Chem Theory Comput; 2016 Apr 12; 12(4):1684-95. PubMed ID: 26938368
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  • 37. 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
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  • 38. The Quality of the Embedding Potential Is Decisive for Minimal Quantum Region Size in Embedding Calculations: The Case of the Green Fluorescent Protein.
    Nåbo LJ, Olsen JMH, Martínez TJ, Kongsted J.
    J Chem Theory Comput; 2017 Dec 12; 13(12):6230-6236. PubMed ID: 29099597
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  • 39. Solvent fluctuations drive the hole transfer in DNA: a mixed quantum-classical study.
    Kubar T, Kleinekathöfer U, Elstner M.
    J Phys Chem B; 2009 Oct 01; 113(39):13107-17. PubMed ID: 19725541
    [Abstract] [Full Text] [Related]

  • 40. 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]

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