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 *

196 related articles for article (PubMed ID: 31115865)

  • 1. Molecular simulations by generalized-ensemble algorithms in isothermal-isobaric ensemble.
    Yamauchi M; Mori Y; Okumura H
    Biophys Rev; 2019 Jun; 11(3):457-469. PubMed ID: 31115865
    [TBL] [Abstract][Full Text] [Related]  

  • 2. Ligand docking simulations by generalized-ensemble algorithms.
    Okamoto Y; Kokubo H; Tanaka T
    Adv Protein Chem Struct Biol; 2013; 92():63-91. PubMed ID: 23954099
    [TBL] [Abstract][Full Text] [Related]  

  • 3. Monte Carlo simulations in generalized isobaric-isothermal ensembles.
    Okumura H; Okamoto Y
    Phys Rev E Stat Nonlin Soft Matter Phys; 2004 Aug; 70(2 Pt 2):026702. PubMed ID: 15447615
    [TBL] [Abstract][Full Text] [Related]  

  • 4. Multibaric-multithermal ensemble molecular dynamics simulations.
    Okumura H; Okamoto Y
    J Comput Chem; 2006 Feb; 27(3):379-95. PubMed ID: 16381079
    [TBL] [Abstract][Full Text] [Related]  

  • 5. Development of isothermal-isobaric replica-permutation method for molecular dynamics and Monte Carlo simulations and its application to reveal temperature and pressure dependence of folded, misfolded, and unfolded states of chignolin.
    Yamauchi M; Okumura H
    J Chem Phys; 2017 Nov; 147(18):184107. PubMed ID: 29141431
    [TBL] [Abstract][Full Text] [Related]  

  • 6. Generalized-ensemble algorithms: enhanced sampling techniques for Monte Carlo and molecular dynamics simulations.
    Okamoto Y
    J Mol Graph Model; 2004 May; 22(5):425-39. PubMed ID: 15099838
    [TBL] [Abstract][Full Text] [Related]  

  • 7. Generalized-ensemble algorithms for molecular simulations of biopolymers.
    Mitsutake A; Sugita Y; Okamoto Y
    Biopolymers; 2001; 60(2):96-123. PubMed ID: 11455545
    [TBL] [Abstract][Full Text] [Related]  

  • 8. Enhanced sampling algorithms.
    Mitsutake A; Mori Y; Okamoto Y
    Methods Mol Biol; 2013; 924():153-95. PubMed ID: 23034749
    [TBL] [Abstract][Full Text] [Related]  

  • 9. Approaches for Controlling the Temperature and Pressure Range in Generalized NPT Ensembles.
    Doi H; Yasuoka K
    J Chem Theory Comput; 2015 Sep; 11(9):4370-6. PubMed ID: 26575930
    [TBL] [Abstract][Full Text] [Related]  

  • 10. Protein folding simulations by generalized-ensemble algorithms.
    Yoda T; Sugita Y; Okamoto Y
    Adv Exp Med Biol; 2014; 805():1-27. PubMed ID: 24446355
    [TBL] [Abstract][Full Text] [Related]  

  • 11. All-Atom Molecular Dynamics Simulation Methods for the Aggregation of Protein and Peptides: Replica Exchange/Permutation and Nonequilibrium Simulations.
    Itoh SG; Okumura H
    Methods Mol Biol; 2022; 2340():197-220. PubMed ID: 35167076
    [TBL] [Abstract][Full Text] [Related]  

  • 12. Configurational constant pressure molecular dynamics.
    Braga C; Travis KP
    J Chem Phys; 2006 Mar; 124(10):104102. PubMed ID: 16542063
    [TBL] [Abstract][Full Text] [Related]  

  • 13. Multidimensional generalized-ensemble algorithms for complex systems.
    Mitsutake A; Okamoto Y
    J Chem Phys; 2009 Jun; 130(21):214105. PubMed ID: 19508054
    [TBL] [Abstract][Full Text] [Related]  

  • 14. Use of the Weighted Histogram Analysis Method for the Analysis of Simulated and Parallel Tempering Simulations.
    Chodera JD; Swope WC; Pitera JW; Seok C; Dill KA
    J Chem Theory Comput; 2007 Jan; 3(1):26-41. PubMed ID: 26627148
    [TBL] [Abstract][Full Text] [Related]  

  • 15. Simulation studies of the fidelity of biomolecular structure ensemble recreation.
    Lätzer J; Eastwood MP; Wolynes PG
    J Chem Phys; 2006 Dec; 125(21):214905. PubMed ID: 17166047
    [TBL] [Abstract][Full Text] [Related]  

  • 16. Simulated Tempering Distributed Replica Sampling, Virtual Replica Exchange, and Other Generalized-Ensemble Methods for Conformational Sampling.
    Rauscher S; Neale C; Pomès R
    J Chem Theory Comput; 2009 Oct; 5(10):2640-62. PubMed ID: 26631779
    [TBL] [Abstract][Full Text] [Related]  

  • 17. Replica sub-permutation method for molecular dynamics and monte carlo simulations.
    Yamauchi M; Okumura H
    J Comput Chem; 2019 Dec; 40(31):2694-2711. PubMed ID: 31365132
    [TBL] [Abstract][Full Text] [Related]  

  • 18. Drug design by generalized-ensemble simulations.
    Okamoto Y
    Curr Pharm Des; 2011; 17(17):1758-72. PubMed ID: 21619524
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Simulated-tempering replica-exchange method for the multidimensional version.
    Mitsutake A
    J Chem Phys; 2009 Sep; 131(9):094105. PubMed ID: 19739847
    [TBL] [Abstract][Full Text] [Related]  

  • 20. Surface-Tension Replica-Exchange Molecular Dynamics Method for Enhanced Sampling of Biological Membrane Systems.
    Mori T; Jung J; Sugita Y
    J Chem Theory Comput; 2013 Dec; 9(12):5629-40. PubMed ID: 26592297
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 10.