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 *

155 related articles for article (PubMed ID: 20499948)

  • 1. On relation between the free-energy perturbation and Bennett's acceptance ratio methods: Tracing the influence of the energy gap.
    Luzhkov VB
    J Chem Phys; 2010 May; 132(19):194104. PubMed ID: 20499948
    [TBL] [Abstract][Full Text] [Related]  

  • 2. Unorthodox uses of Bennett's acceptance ratio method.
    König G; Bruckner S; Boresch S
    J Comput Chem; 2009 Aug; 30(11):1712-8. PubMed ID: 19373838
    [TBL] [Abstract][Full Text] [Related]  

  • 3. Bennett's acceptance ratio and histogram analysis methods enhanced by umbrella sampling along a reaction coordinate in configurational space.
    Kim I; Allen TW
    J Chem Phys; 2012 Apr; 136(16):164103. PubMed ID: 22559466
    [TBL] [Abstract][Full Text] [Related]  

  • 4. Efficiency of alchemical free energy simulations. I. A practical comparison of the exponential formula, thermodynamic integration, and Bennett's acceptance ratio method.
    Bruckner S; Boresch S
    J Comput Chem; 2011 May; 32(7):1303-19. PubMed ID: 21425288
    [TBL] [Abstract][Full Text] [Related]  

  • 5. Accurate calculations of free-energy differences by the distribution method.
    Wu D
    J Chem Phys; 2008 Jun; 128(22):224105. PubMed ID: 18554004
    [TBL] [Abstract][Full Text] [Related]  

  • 6. Improving the efficiency and reliability of free energy perturbation calculations using overlap sampling methods.
    Lu N; Kofke DA; Woolf TB
    J Comput Chem; 2004 Jan; 25(1):28-39. PubMed ID: 14634991
    [TBL] [Abstract][Full Text] [Related]  

  • 7. Suitability of umbrella- and overlap-sampling methods for calculation of solid-phase free energies by molecular simulation.
    Tan TB; Schultz AJ; Kofke DA
    J Chem Phys; 2010 Jun; 132(21):214103. PubMed ID: 20528014
    [TBL] [Abstract][Full Text] [Related]  

  • 8. Avoiding the van der Waals endpoint problem using serial atomic insertion.
    Boresch S; Bruckner S
    J Comput Chem; 2011 Aug; 32(11):2449-58. PubMed ID: 21607991
    [TBL] [Abstract][Full Text] [Related]  

  • 9. Free energy profiles of amino acid side chain analogs near water-vapor interface obtained via MD simulations.
    Shaytan AK; Ivanov VA; Shaitan KV; Khokhlov AR
    J Comput Chem; 2010 Jan; 31(1):204-16. PubMed ID: 19421988
    [TBL] [Abstract][Full Text] [Related]  

  • 10. Non-Boltzmann sampling and Bennett's acceptance ratio method: how to profit from bending the rules.
    König G; Boresch S
    J Comput Chem; 2011 Apr; 32(6):1082-90. PubMed ID: 21387335
    [TBL] [Abstract][Full Text] [Related]  

  • 11. Free energy perturbation study of water dimer dissociation kinetics.
    Ming Y; Lai G; Tong C; Wood RH; Doren DJ
    J Chem Phys; 2004 Jul; 121(2):773-7. PubMed ID: 15260604
    [TBL] [Abstract][Full Text] [Related]  

  • 12. Assessment of nonequilibrium free energy methods.
    Cossins BP; Foucher S; Edge CM; Essex JW
    J Phys Chem B; 2009 Apr; 113(16):5508-19. PubMed ID: 19368411
    [TBL] [Abstract][Full Text] [Related]  

  • 13. Hydration free energies of monovalent ions in transferable intermolecular potential four point fluctuating charge water: an assessment of simulation methodology and force field performance and transferability.
    Warren GL; Patel S
    J Chem Phys; 2007 Aug; 127(6):064509. PubMed ID: 17705614
    [TBL] [Abstract][Full Text] [Related]  

  • 14. Calculation of free-energy differences and potentials of mean force by a multi-energy gap method.
    Zhou HX
    J Chem Phys; 2008 Mar; 128(11):114104. PubMed ID: 18361551
    [TBL] [Abstract][Full Text] [Related]  

  • 15. 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; 111(23):6425-36. PubMed ID: 17508737
    [TBL] [Abstract][Full Text] [Related]  

  • 16. Efficient calculation of temperature dependence of solid-phase free energies by overlap sampling coupled with harmonically targeted perturbation.
    Tan TB; Schultz AJ; Kofke DA
    J Chem Phys; 2010 Oct; 133(13):134104. PubMed ID: 20942520
    [TBL] [Abstract][Full Text] [Related]  

  • 17. Comparison of efficiency and bias of free energies computed by exponential averaging, the Bennett acceptance ratio, and thermodynamic integration.
    Shirts MR; Pande VS
    J Chem Phys; 2005 Apr; 122(14):144107. PubMed ID: 15847516
    [TBL] [Abstract][Full Text] [Related]  

  • 18. On the use of Bennett's acceptance ratio method in multi-canonical-type simulations.
    Fenwick MK; Escobedo FA
    J Chem Phys; 2004 Feb; 120(7):3066-74. PubMed ID: 15268459
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Absolute and relative binding free energy calculations of the interaction of biotin and its analogs with streptavidin using molecular dynamics/free energy perturbation approaches.
    Miyamoto S; Kollman PA
    Proteins; 1993 Jul; 16(3):226-45. PubMed ID: 8346190
    [TBL] [Abstract][Full Text] [Related]  

  • 20. Absolute binding free energy calculations of CBClip host-guest systems in the SAMPL5 blind challenge.
    Lee J; Tofoleanu F; Pickard FC; König G; Huang J; Damjanović A; Baek M; Seok C; Brooks BR
    J Comput Aided Mol Des; 2017 Jan; 31(1):71-85. PubMed ID: 27677749
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 8.