These tools will no longer be maintained as of December 31, 2024. Archived website can be found here. PubMed4Hh GitHub repository can be found here. Contact NLM Customer Service if you have questions.


BIOMARKERS

Molecular Biopsy of Human Tumors

- a resource for Precision Medicine *

151 related articles for article (PubMed ID: 17391023)

  • 21. A quantum chemical approach to the free energy calculations in condensed systems: the QM/MM method combined with the theory of energy representation.
    Takahashi H; Matubayasi N; Nakahara M; Nitta T
    J Chem Phys; 2004 Sep; 121(9):3989-99. PubMed ID: 15332945
    [TBL] [Abstract][Full Text] [Related]  

  • 22. QM-MM interactions in simulations of liquid water using combined semi-empirical/classical Hamiltonians.
    Geerke DP; Thiel S; Thiel W; van Gunsteren WF
    Phys Chem Chem Phys; 2008 Jan; 10(2):297-302. PubMed ID: 18213415
    [TBL] [Abstract][Full Text] [Related]  

  • 23. 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; 118(46):13217-25. PubMed ID: 25340948
    [TBL] [Abstract][Full Text] [Related]  

  • 24. Cation solvation with quantum chemical effects modeled by a size-consistent multi-partitioning quantum mechanics/molecular mechanics method.
    Watanabe HC; Kubillus M; Kubař T; Stach R; Mizaikoff B; Ishikita H
    Phys Chem Chem Phys; 2017 Jul; 19(27):17985-17997. PubMed ID: 28664950
    [TBL] [Abstract][Full Text] [Related]  

  • 25. A modified QM/MM Hamiltonian with the Self-Consistent-Charge Density-Functional-Tight-Binding Theory for highly charged QM regions.
    Hou G; Zhu X; Elstner M; Cui Q
    J Chem Theory Comput; 2012 Nov; 8(11):4293-4304. PubMed ID: 23275762
    [TBL] [Abstract][Full Text] [Related]  

  • 26. Toward a consistent treatment of polarization in model QM/MM calculations.
    Illingworth CJ; Parkes KE; Snell CR; Ferenczy GG; Reynolds CA
    J Phys Chem A; 2008 Nov; 112(47):12151-6. PubMed ID: 18986123
    [TBL] [Abstract][Full Text] [Related]  

  • 27. Solvatochromic shifts of polar and non-polar molecules in ambient and supercritical water: a sequential quantum mechanics/molecular mechanics study including solute-solvent electron exchange-correlation.
    Ma H; Ma Y
    J Chem Phys; 2012 Dec; 137(21):214504. PubMed ID: 23231248
    [TBL] [Abstract][Full Text] [Related]  

  • 28. Do Better Quality Embedding Potentials Accelerate the Convergence of QM/MM Models? The Case of Solvated Acid Clusters.
    Ho J; Shao Y; Kato J
    Molecules; 2018 Sep; 23(10):. PubMed ID: 30261616
    [TBL] [Abstract][Full Text] [Related]  

  • 29. Computation of the free energy due to electron density fluctuation of a solute in solution: a QM/MM method with perturbation approach combined with a theory of solutions.
    Suzuoka D; Takahashi H; Morita A
    J Chem Phys; 2014 Apr; 140(13):134111. PubMed ID: 24712784
    [TBL] [Abstract][Full Text] [Related]  

  • 30. Performance of the AMOEBA Water Model in the Vicinity of QM Solutes: A Diagnosis Using Energy Decomposition Analysis.
    Mao Y; Shao Y; Dziedzic J; Skylaris CK; Head-Gordon T; Head-Gordon M
    J Chem Theory Comput; 2017 May; 13(5):1963-1979. PubMed ID: 28430427
    [TBL] [Abstract][Full Text] [Related]  

  • 31. Orbital-free QM/MM simulation combined with a theory of solutions.
    Takahashi H
    J Chem Phys; 2023 Sep; 159(12):. PubMed ID: 38127397
    [TBL] [Abstract][Full Text] [Related]  

  • 32. Description of phosphate hydrolysis reactions with the Self-Consistent-Charge Density-Functional-Tight-Binding (SCC-DFTB) theory. 1. Parameterization.
    Yang Y; Yu H; York D; Elstner M; Cui Q
    J Chem Theory Comput; 2008; 4(12):2067-2084. PubMed ID: 19352441
    [TBL] [Abstract][Full Text] [Related]  

  • 33. QM/MM simulation of liquid water with an adaptive quantum region.
    Bernstein N; Várnai C; Solt I; Winfield SA; Payne MC; Simon I; Fuxreiter M; Csányi G
    Phys Chem Chem Phys; 2012 Jan; 14(2):646-56. PubMed ID: 22089416
    [TBL] [Abstract][Full Text] [Related]  

  • 34. An improvement in quantum mechanical description of solute-solvent interactions in condensed systems via the number-adaptive multiscale quantum mechanical/molecular mechanical-molecular dynamics method: application to zwitterionic glycine in aqueous solution.
    Takenaka N; Kitamura Y; Koyano Y; Nagaoka M
    J Chem Phys; 2012 Jul; 137(2):024501. PubMed ID: 22803541
    [TBL] [Abstract][Full Text] [Related]  

  • 35. The self-consistent charge density functional tight binding method applied to liquid water and the hydrated excess proton: benchmark simulations.
    Maupin CM; Aradi B; Voth GA
    J Phys Chem B; 2010 May; 114(20):6922-31. PubMed ID: 20426461
    [TBL] [Abstract][Full Text] [Related]  

  • 36. Modeling the structure and absorption spectra of stilbazolium merocyanine in polar and nonpolar solvents using hybrid QM/MM techniques.
    Murugan NA; Kongsted J; Rinkevicius Z; Aidas K; Ågren H
    J Phys Chem B; 2010 Oct; 114(42):13349-57. PubMed ID: 20925401
    [TBL] [Abstract][Full Text] [Related]  

  • 37. Analysis of the conformational properties of amine ligands at the gold/water interface with QM, MM and QM/MM simulations.
    Liang D; Hong J; Fang D; Bennett JW; Mason SE; Hamers RJ; Cui Q
    Phys Chem Chem Phys; 2018 Jan; 20(5):3349-3362. PubMed ID: 29226924
    [TBL] [Abstract][Full Text] [Related]  

  • 38. Quantifying the mechanism of phosphate monoester hydrolysis in aqueous solution by evaluating the relevant ab initio QM/MM free-energy surfaces.
    Plotnikov NV; Prasad BR; Chakrabarty S; Chu ZT; Warshel A
    J Phys Chem B; 2013 Oct; 117(42):12807-19. PubMed ID: 23601038
    [TBL] [Abstract][Full Text] [Related]  

  • 39. Comparison of linear-scaling semiempirical methods and combined quantum mechanical/molecular mechanical methods for enzymic reactions. II. An energy decomposition analysis.
    Titmuss SJ; Cummins PL; Rendell AP; Bliznyuk AA; Gready JE
    J Comput Chem; 2002 Nov; 23(14):1314-22. PubMed ID: 12214314
    [TBL] [Abstract][Full Text] [Related]  

  • 40. Free-energy analysis of the electron-density fluctuation in the quantum-mechanical/molecular-mechanical simulation combined with the theory of energy representation.
    Matubayasi N; Takahashi H
    J Chem Phys; 2012 Jan; 136(4):044505. PubMed ID: 22299889
    [TBL] [Abstract][Full Text] [Related]  

    [Previous]   [Next]    [New Search]
    of 8.