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 *

240 related articles for article (PubMed ID: 25705140)

  • 1. Conformational sampling of oligosaccharides using Hamiltonian replica exchange with two-dimensional dihedral biasing potentials and the weighted histogram analysis method (WHAM).
    Yang M; MacKerell AD
    J Chem Theory Comput; 2015 Feb; 11(2):788-99. PubMed ID: 25705140
    [TBL] [Abstract][Full Text] [Related]  

  • 2. Enhanced conformational sampling using replica exchange with concurrent solute scaling and hamiltonian biasing realized in one dimension.
    Yang M; Huang J; MacKerell AD
    J Chem Theory Comput; 2015 Jun; 11(6):2855-67. PubMed ID: 26082676
    [TBL] [Abstract][Full Text] [Related]  

  • 3. Enhanced conformational sampling of carbohydrates by Hamiltonian replica-exchange simulation.
    Mishra SK; Kara M; Zacharias M; Koca J
    Glycobiology; 2014 Jan; 24(1):70-84. PubMed ID: 24134878
    [TBL] [Abstract][Full Text] [Related]  

  • 4. Hamiltonian replica exchange combined with elastic network analysis to enhance global domain motions in atomistic molecular dynamics simulations.
    Ostermeir K; Zacharias M
    Proteins; 2014 Dec; 82(12):3410-9. PubMed ID: 25243707
    [TBL] [Abstract][Full Text] [Related]  

  • 5. Adaptive Biasing Combined with Hamiltonian Replica Exchange to Improve Umbrella Sampling Free Energy Simulations.
    Zeller F; Zacharias M
    J Chem Theory Comput; 2014 Feb; 10(2):703-10. PubMed ID: 26580047
    [TBL] [Abstract][Full Text] [Related]  

  • 6. Conformational properties of glucose-based disaccharides investigated using molecular dynamics simulations with local elevation umbrella sampling.
    Perić-Hassler L; Hansen HS; Baron R; Hünenberger PH
    Carbohydr Res; 2010 Aug; 345(12):1781-801. PubMed ID: 20576257
    [TBL] [Abstract][Full Text] [Related]  

  • 7. Hamiltonian replica-exchange simulations with adaptive biasing of peptide backbone and side chain dihedral angles.
    Ostermeir K; Zacharias M
    J Comput Chem; 2014 Jan; 35(2):150-8. PubMed ID: 24318649
    [TBL] [Abstract][Full Text] [Related]  

  • 8. Enhanced conformational sampling of nucleic acids by a new Hamiltonian replica exchange molecular dynamics approach.
    Curuksu J; Zacharias M
    J Chem Phys; 2009 Mar; 130(10):104110. PubMed ID: 19292526
    [TBL] [Abstract][Full Text] [Related]  

  • 9. Enhanced Conformational Sampling of N-Glycans in Solution with Replica State Exchange Metadynamics.
    Galvelis R; Re S; Sugita Y
    J Chem Theory Comput; 2017 May; 13(5):1934-1942. PubMed ID: 28399363
    [TBL] [Abstract][Full Text] [Related]  

  • 10. Modeling of Oligosaccharides within Glycoproteins from Free-Energy Landscapes.
    Turupcu A; Oostenbrink C
    J Chem Inf Model; 2017 Sep; 57(9):2222-2236. PubMed ID: 28816453
    [TBL] [Abstract][Full Text] [Related]  

  • 11. Boosting the conformational sampling by combining replica exchange with solute tempering and well-sliced metadynamics.
    Kapakayala AB; Nair NN
    J Comput Chem; 2021 Dec; 42(31):2233-2240. PubMed ID: 34585768
    [TBL] [Abstract][Full Text] [Related]  

  • 12. Conformational properties of α- or β-(1→6)-linked oligosaccharides: Hamiltonian replica exchange MD simulations and NMR experiments.
    Patel DS; Pendrill R; Mallajosyula SS; Widmalm G; MacKerell AD
    J Phys Chem B; 2014 Mar; 118(11):2851-71. PubMed ID: 24552401
    [TBL] [Abstract][Full Text] [Related]  

  • 13. 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]  

  • 14. Enhanced sampling of peptide and protein conformations using replica exchange simulations with a peptide backbone biasing-potential.
    Kannan S; Zacharias M
    Proteins; 2007 Feb; 66(3):697-706. PubMed ID: 17120231
    [TBL] [Abstract][Full Text] [Related]  

  • 15. Ball-and-Stick Local Elevation Umbrella Sampling: Molecular Simulations Involving Enhanced Sampling within Conformational or Alchemical Subspaces of Low Internal Dimensionalities, Minimal Irrelevant Volumes, and Problem-Adapted Geometries.
    Hansen HS; Hünenberger PH
    J Chem Theory Comput; 2010 Sep; 6(9):2622-46. PubMed ID: 26616065
    [TBL] [Abstract][Full Text] [Related]  

  • 16. Replica-Exchange Methods for Biomolecular Simulations.
    Sugita Y; Kamiya M; Oshima H; Re S
    Methods Mol Biol; 2019; 2022():155-177. PubMed ID: 31396903
    [TBL] [Abstract][Full Text] [Related]  

  • 17. Multiple scaling replica exchange for the conformational sampling of biomolecules in explicit water.
    Kamberaj H; van der Vaart A
    J Chem Phys; 2007 Dec; 127(23):234102. PubMed ID: 18154370
    [TBL] [Abstract][Full Text] [Related]  

  • 18. Preferred conformations of N-glycan core pentasaccharide in solution and in glycoproteins.
    Jo S; Qi Y; Im W
    Glycobiology; 2016 Jan; 26(1):19-29. PubMed ID: 26405106
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Comparison of the umbrella sampling and the double decoupling method in binding free energy predictions for SAMPL6 octa-acid host-guest challenges.
    Nishikawa N; Han K; Wu X; Tofoleanu F; Brooks BR
    J Comput Aided Mol Des; 2018 Oct; 32(10):1075-1086. PubMed ID: 30324304
    [TBL] [Abstract][Full Text] [Related]  

  • 20. Molecular dynamics simulation of Lewis blood groups and related oligosaccharides.
    Mukhopadhyay C; Bush CA
    Biopolymers; 1991 Dec; 31(14):1737-46. PubMed ID: 1793812
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 12.