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 *

127 related articles for article (PubMed ID: 29464736)

  • 1. Molecular dynamics coupled with a virtual system for effective conformational sampling.
    Hayami T; Kasahara K; Nakamura H; Higo J
    J Comput Chem; 2018 Jul; 39(19):1291-1299. PubMed ID: 29464736
    [TBL] [Abstract][Full Text] [Related]  

  • 2. Multidimensional virtual-system coupled canonical molecular dynamics to compute free-energy landscapes of peptide multimer assembly.
    Hayami T; Higo J; Nakamura H; Kasahara K
    J Comput Chem; 2019 Oct; 40(28):2453-2463. PubMed ID: 31282023
    [TBL] [Abstract][Full Text] [Related]  

  • 3. GA-guided mD-VcMD: A genetic-algorithm-guided method for multi-dimensional virtual-system coupled molecular dynamics.
    Higo J; Kusaka A; Kasahara K; Kamiya N; Hayato I; Qilin X; Takahashi T; Fukuda I; Mori K; Hata Y; Fukunishi Y
    Biophys Physicobiol; 2020; 17():161-176. PubMed ID: 33585149
    [TBL] [Abstract][Full Text] [Related]  

  • 4. Virtual-system-coupled adaptive umbrella sampling to compute free-energy landscape for flexible molecular docking.
    Higo J; Dasgupta B; Mashimo T; Kasahara K; Fukunishi Y; Nakamura H
    J Comput Chem; 2015 Jul; 36(20):1489-501. PubMed ID: 26045390
    [TBL] [Abstract][Full Text] [Related]  

  • 5. myPresto/omegagene 2020: a molecular dynamics simulation engine for virtual-system coupled sampling.
    Kasahara K; Terazawa H; Itaya H; Goto S; Nakamura H; Takahashi T; Higo J
    Biophys Physicobiol; 2020; 17():140-146. PubMed ID: 33240741
    [TBL] [Abstract][Full Text] [Related]  

  • 6. A virtual-system coupled multicanonical molecular dynamics simulation: principles and applications to free-energy landscape of protein-protein interaction with an all-atom model in explicit solvent.
    Higo J; Umezawa K; Nakamura H
    J Chem Phys; 2013 May; 138(18):184106. PubMed ID: 23676028
    [TBL] [Abstract][Full Text] [Related]  

  • 7. Virtual states introduced for overcoming entropic barriers in conformational space.
    Higo J; Nakamura H
    Biophysics (Nagoya-shi); 2012; 8():139-44. PubMed ID: 27493530
    [TBL] [Abstract][Full Text] [Related]  

  • 8. Enhanced and effective conformational sampling of protein molecular systems for their free energy landscapes.
    Higo J; Ikebe J; Kamiya N; Nakamura H
    Biophys Rev; 2012 Mar; 4(1):27-44. PubMed ID: 22347892
    [TBL] [Abstract][Full Text] [Related]  

  • 9. Enhanced Conformational Sampling in Molecular Dynamics Simulations of Solvated Peptides: Fragment-Based Local Elevation Umbrella Sampling.
    Hansen HS; Daura X; Hünenberger PH
    J Chem Theory Comput; 2010 Sep; 6(9):2598-621. PubMed ID: 26616064
    [TBL] [Abstract][Full Text] [Related]  

  • 10. Multi-dimensional virtual system introduced to enhance canonical sampling.
    Higo J; Kasahara K; Nakamura H
    J Chem Phys; 2017 Oct; 147(13):134102. PubMed ID: 28987097
    [TBL] [Abstract][Full Text] [Related]  

  • 11. Enhancement of canonical sampling by virtual-state transitions.
    Higo J; Kasahara K; Dasgupta B; Nakamura H
    J Chem Phys; 2017 Jan; 146(4):044104. PubMed ID: 28147529
    [TBL] [Abstract][Full Text] [Related]  

  • 12. Adaptive lambda square dynamics simulation: an efficient conformational sampling method for biomolecules.
    Ikebe J; Sakuraba S; Kono H
    J Comput Chem; 2014 Jan; 35(1):39-50. PubMed ID: 24166005
    [TBL] [Abstract][Full Text] [Related]  

  • 13. Free-energy analyses of a proton transfer reaction by simulated-tempering umbrella sampling and first-principles molecular dynamics simulations.
    Mori Y; Okamoto Y
    Phys Rev E Stat Nonlin Soft Matter Phys; 2013 Feb; 87(2):023301. PubMed ID: 23496633
    [TBL] [Abstract][Full Text] [Related]  

  • 14. Enhanced sampling simulations to construct free-energy landscape of protein-partner substrate interaction.
    Ikebe J; Umezawa K; Higo J
    Biophys Rev; 2016 Mar; 8(1):45-62. PubMed ID: 28510144
    [TBL] [Abstract][Full Text] [Related]  

  • 15. Thermodynamics of Protein Folding Studied by Umbrella Sampling along a Reaction Coordinate of Native Contacts.
    Meshkin H; Zhu F
    J Chem Theory Comput; 2017 May; 13(5):2086-2097. PubMed ID: 28355066
    [TBL] [Abstract][Full Text] [Related]  

  • 16. Temperature-Accelerated Sampling and Amplified Collective Motion with Adiabatic Reweighting to Obtain Canonical Distributions and Ensemble Averages.
    Hu Y; Hong W; Shi Y; Liu H
    J Chem Theory Comput; 2012 Oct; 8(10):3777-92. PubMed ID: 26593019
    [TBL] [Abstract][Full Text] [Related]  

  • 17. A method for predicting protein conformational pathways by using molecular dynamics simulations guided by difference distance matrices.
    Yonezawa Y
    J Comput Chem; 2016 May; 37(13):1139-46. PubMed ID: 26804151
    [TBL] [Abstract][Full Text] [Related]  

  • 18. Free energy calculation using molecular dynamics simulation combined with the three-dimensional reference interaction site model theory. II. Thermodynamic integration along a spatial reaction coordinate.
    Miyata T; Ikuta Y; Hirata F
    J Chem Phys; 2011 Jan; 134(4):044127. PubMed ID: 21280707
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Combine umbrella sampling with integrated tempering method for efficient and accurate calculation of free energy changes of complex energy surface.
    Yang M; Yang L; Gao Y; Hu H
    J Chem Phys; 2014 Jul; 141(4):044108. PubMed ID: 25084882
    [TBL] [Abstract][Full Text] [Related]  

  • 20. Calculating Position-Dependent Diffusivity in Biased Molecular Dynamics Simulations.
    Comer J; Chipot C; González-Nilo FD
    J Chem Theory Comput; 2013 Feb; 9(2):876-82. PubMed ID: 26588731
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 7.