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 *

255 related articles for article (PubMed ID: 23925979)

  • 1. Hamiltonian replica-permutation method and its applications to an alanine dipeptide and amyloid-β(29-42) peptides.
    Itoh SG; Okumura H
    J Comput Chem; 2013 Nov; 34(29):2493-7. PubMed ID: 23925979
    [TBL] [Abstract][Full Text] [Related]  

  • 2. A convective replica-exchange method for sampling new energy basins.
    Spill YG; Bouvier G; Nilges M
    J Comput Chem; 2013 Jan; 34(2):132-40. PubMed ID: 22961200
    [TBL] [Abstract][Full Text] [Related]  

  • 3. Coulomb replica-exchange method: handling electrostatic attractive and repulsive forces for biomolecules.
    Itoh SG; Okumura H
    J Comput Chem; 2013 Mar; 34(8):622-39. PubMed ID: 23197415
    [TBL] [Abstract][Full Text] [Related]  

  • 4. Replica-Permutation Method with the Suwa-Todo Algorithm beyond the Replica-Exchange Method.
    Itoh SG; Okumura H
    J Chem Theory Comput; 2013 Jan; 9(1):570-81. PubMed ID: 26589055
    [TBL] [Abstract][Full Text] [Related]  

  • 5. Dimerization process of amyloid-β(29-42) studied by the Hamiltonian replica-permutation molecular dynamics simulations.
    Itoh SG; Okumura H
    J Phys Chem B; 2014 Oct; 118(39):11428-36. PubMed ID: 25192386
    [TBL] [Abstract][Full Text] [Related]  

  • 6. Replica permutation with solute tempering for molecular dynamics simulation and its application to the dimerization of amyloid-β fragments.
    Fukuhara D; Itoh SG; Okumura H
    J Chem Phys; 2022 Feb; 156(8):084109. PubMed ID: 35232199
    [TBL] [Abstract][Full Text] [Related]  

  • 7. Replica state exchange metadynamics for improving the convergence of free energy estimates.
    Galvelis R; Sugita Y
    J Comput Chem; 2015 Jul; 36(19):1446-55. PubMed ID: 25990969
    [TBL] [Abstract][Full Text] [Related]  

  • 8. On easy implementation of a variant of the replica exchange with solute tempering in GROMACS.
    Terakawa T; Kameda T; Takada S
    J Comput Chem; 2011 May; 32(7):1228-34. PubMed ID: 21425280
    [TBL] [Abstract][Full Text] [Related]  

  • 9. Replica exchange with solute tempering: a method for sampling biological systems in explicit water.
    Liu P; Kim B; Friesner RA; Berne BJ
    Proc Natl Acad Sci U S A; 2005 Sep; 102(39):13749-54. PubMed ID: 16172406
    [TBL] [Abstract][Full Text] [Related]  

  • 10. Replica-exchange method in van der Waals radius space: overcoming steric restrictions for biomolecules.
    Itoh SG; Okumura H; Okamoto Y
    J Chem Phys; 2010 Apr; 132(13):134105. PubMed ID: 20387919
    [TBL] [Abstract][Full Text] [Related]  

  • 11. 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]  

  • 12. 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]  

  • 13. Comparison of molecular dynamics simulation methods for amyloid β(1-42) monomers containing D-aspartic acid residues for predicting retention times in chromatography.
    Oda A; Kobayashi K; Takahashi O
    J Chromatogr B Analyt Technol Biomed Life Sci; 2011 Nov; 879(29):3337-43. PubMed ID: 21871847
    [TBL] [Abstract][Full Text] [Related]  

  • 14. Communication: Simulated tempering with fast on-the-fly weight determination.
    Nguyen PH; Okamoto Y; Derreumaux P
    J Chem Phys; 2013 Feb; 138(6):061102. PubMed ID: 23425452
    [TBL] [Abstract][Full Text] [Related]  

  • 15. TIGER2: an improved algorithm for temperature intervals with global exchange of replicas.
    Li X; Latour RA; Stuart SJ
    J Chem Phys; 2009 May; 130(17):174106. PubMed ID: 19425768
    [TBL] [Abstract][Full Text] [Related]  

  • 16. Effects of all-atom force fields on amyloid oligomerization: replica exchange molecular dynamics simulations of the Aβ(16-22) dimer and trimer.
    Nguyen PH; Li MS; Derreumaux P
    Phys Chem Chem Phys; 2011 May; 13(20):9778-88. PubMed ID: 21487594
    [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. Effects of G33A and G33I mutations on the structures of monomer and dimer of the amyloid-β fragment 29-42 by replica exchange molecular dynamics simulations.
    Lu Y; Wei G; Derreumaux P
    J Phys Chem B; 2011 Feb; 115(5):1282-8. PubMed ID: 21186801
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Enhanced exchange algorithm without detailed balance condition for replica exchange method.
    Kondo HX; Taiji M
    J Chem Phys; 2013 Jun; 138(24):244113. PubMed ID: 23822233
    [TBL] [Abstract][Full Text] [Related]  

  • 20. Spontaneous dimer states of the Aβ(21-30) decapeptide.
    Smith MD; Srinivasa Rao J; Cruz L
    Phys Chem Chem Phys; 2014 Jul; 16(26):13069-73. PubMed ID: 24888358
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 13.