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 *

304 related articles for article (PubMed ID: 25649827)

  • 1. The adaptive buffered force QM/MM method in the CP2K and AMBER software packages.
    Mones L; Jones A; Götz AW; Laino T; Walker RC; Leimkuhler B; Csányi G; Bernstein N
    J Comput Chem; 2015 Apr; 36(9):633-48. PubMed ID: 25649827
    [TBL] [Abstract][Full Text] [Related]  

  • 2. 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]  

  • 3. 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; 128(3):034105. PubMed ID: 18205486
    [TBL] [Abstract][Full Text] [Related]  

  • 4. An extensible interface for QM/MM molecular dynamics simulations with AMBER.
    Götz AW; Clark MA; Walker RC
    J Comput Chem; 2014 Jan; 35(2):95-108. PubMed ID: 24122798
    [TBL] [Abstract][Full Text] [Related]  

  • 5. Interfacing the GROMOS (bio)molecular simulation software to quantum-chemical program packages.
    Meier K; Schmid N; van Gunsteren WF
    J Comput Chem; 2012 Oct; 33(26):2108-17. PubMed ID: 22736402
    [TBL] [Abstract][Full Text] [Related]  

  • 6. The implementation of a fast and accurate QM/MM potential method in Amber.
    Walker RC; Crowley MF; Case DA
    J Comput Chem; 2008 May; 29(7):1019-31. PubMed ID: 18072177
    [TBL] [Abstract][Full Text] [Related]  

  • 7. Accuracy of buffered-force QM/MM simulations of silica.
    Peguiron A; Colombi Ciacchi L; De Vita A; Kermode JR; Moras G
    J Chem Phys; 2015 Feb; 142(6):064116. PubMed ID: 25681896
    [TBL] [Abstract][Full Text] [Related]  

  • 8. VFFDT: A New Software for Preparing AMBER Force Field Parameters for Metal-Containing Molecular Systems.
    Zheng S; Tang Q; He J; Du S; Xu S; Wang C; Xu Y; Lin F
    J Chem Inf Model; 2016 Apr; 56(4):811-8. PubMed ID: 26998926
    [TBL] [Abstract][Full Text] [Related]  

  • 9. Comparison of a QM/MM force field and molecular mechanics force fields in simulations of alanine and glycine "dipeptides" (Ace-Ala-Nme and Ace-Gly-Nme) in water in relation to the problem of modeling the unfolded peptide backbone in solution.
    Hu H; Elstner M; Hermans J
    Proteins; 2003 Feb; 50(3):451-63. PubMed ID: 12557187
    [TBL] [Abstract][Full Text] [Related]  

  • 10. Application of Adaptive QM/MM Methods to Molecular Dynamics Simulations of Aqueous Systems.
    Park K; Götz AW; Walker RC; Paesani F
    J Chem Theory Comput; 2012 Aug; 8(8):2868-77. PubMed ID: 26592126
    [TBL] [Abstract][Full Text] [Related]  

  • 11. Tests of an adaptive QM/MM calculation on free energy profiles of chemical reactions in solution.
    Várnai C; Bernstein N; Mones L; Csányi G
    J Phys Chem B; 2013 Oct; 117(40):12202-11. PubMed ID: 24033146
    [TBL] [Abstract][Full Text] [Related]  

  • 12. Reliable treatment of electrostatics in combined QM/MM simulation of macromolecules.
    Schaefer P; Riccardi D; Cui Q
    J Chem Phys; 2005 Jul; 123(1):014905. PubMed ID: 16035867
    [TBL] [Abstract][Full Text] [Related]  

  • 13. Evaluating boundary dependent errors in QM/MM simulations.
    Solt I; Kulhánek P; Simon I; Winfield S; Payne MC; Csányi G; Fuxreiter M
    J Phys Chem B; 2009 Apr; 113(17):5728-35. PubMed ID: 19341253
    [TBL] [Abstract][Full Text] [Related]  

  • 14. Incorporation of deMon2k as a new parallel quantum mechanical code for the PUPIL system.
    Bertran O; Trickey SB; Torras J
    J Comput Chem; 2010 Nov; 31(14):2669-76. PubMed ID: 20740567
    [TBL] [Abstract][Full Text] [Related]  

  • 15. Convergence of QM/MM free-energy perturbations based on molecular-mechanics or semiempirical simulations.
    Heimdal J; Ryde U
    Phys Chem Chem Phys; 2012 Sep; 14(36):12592-604. PubMed ID: 22797613
    [TBL] [Abstract][Full Text] [Related]  

  • 16. Recent advances toward a general purpose linear-scaling quantum force field.
    Giese TJ; Huang M; Chen H; York DM
    Acc Chem Res; 2014 Sep; 47(9):2812-20. PubMed ID: 24937206
    [TBL] [Abstract][Full Text] [Related]  

  • 17. Mechanism of proteolysis in matrix metalloproteinase-2 revealed by QM/MM modeling.
    Vasilevskaya T; Khrenova MG; Nemukhin AV; Thiel W
    J Comput Chem; 2015 Aug; 36(21):1621-30. PubMed ID: 26132652
    [TBL] [Abstract][Full Text] [Related]  

  • 18. Quantum Mechanics/Molecular Mechanics Simulations on NVIDIA and AMD Graphics Processing Units.
    Manathunga M; Aktulga HM; Götz AW; Merz KM
    J Chem Inf Model; 2023 Feb; 63(3):711-717. PubMed ID: 36720086
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Hybrid Quantum Mechanics/Molecular Mechanics/Coarse Grained Modeling: A Triple-Resolution Approach for Biomolecular Systems.
    Sokkar P; Boulanger E; Thiel W; Sanchez-Garcia E
    J Chem Theory Comput; 2015 Apr; 11(4):1809-18. PubMed ID: 26574388
    [TBL] [Abstract][Full Text] [Related]  

  • 20. A Practical Quantum Mechanics Molecular Mechanics Method for the Dynamical Study of Reactions in Biomolecules.
    Mendieta-Moreno JI; Marcos-Alcalde I; Trabada DG; Gómez-Puertas P; Ortega J; Mendieta J
    Adv Protein Chem Struct Biol; 2015; 100():67-88. PubMed ID: 26415841
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 16.