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185 related items for PubMed ID: 35167076

  • 1. 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
    [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
    [Abstract] [Full Text] [Related]

  • 3. Replica Exchange Molecular Dynamics: A Practical Application Protocol with Solutions to Common Problems and a Peptide Aggregation and Self-Assembly Example.
    Qi R, Wei G, Ma B, Nussinov R.
    Methods Mol Biol; 2018; 1777():101-119. PubMed ID: 29744830
    [Abstract] [Full Text] [Related]

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

  • 5. 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
    [Abstract] [Full Text] [Related]

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

  • 7.
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  • 8. Protein folding simulations by generalized-ensemble algorithms.
    Yoda T, Sugita Y, Okamoto Y.
    Adv Exp Med Biol; 2014 Jun; 805():1-27. PubMed ID: 24446355
    [Abstract] [Full Text] [Related]

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

  • 10. 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 14; 147(18):184107. PubMed ID: 29141431
    [Abstract] [Full Text] [Related]

  • 11. 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 01; 879(29):3337-43. PubMed ID: 21871847
    [Abstract] [Full Text] [Related]

  • 12. Transformation of a design peptide between the α-helix and β-hairpin structures using a helix-strand replica-exchange molecular dynamics simulation.
    Okumura H, Itoh SG.
    Phys Chem Chem Phys; 2013 Sep 07; 15(33):13852-61. PubMed ID: 23839056
    [Abstract] [Full Text] [Related]

  • 13. Dimerization of α-Synuclein Fragments Studied by Isothermal-Isobaric Replica-Permutation Molecular Dynamics Simulation.
    Yamauchi M, Okumura H.
    J Chem Inf Model; 2021 Mar 22; 61(3):1307-1321. PubMed ID: 33625841
    [Abstract] [Full Text] [Related]

  • 14. Enhanced sampling using replica exchange with nonequilibrium switches: A case study on simple models.
    Badani S, Krishnan M.
    J Chem Phys; 2022 Nov 14; 157(18):184102. PubMed ID: 36379798
    [Abstract] [Full Text] [Related]

  • 15. Norepinephrine Inhibits Alzheimer's Amyloid-β Peptide Aggregation and Destabilizes Amyloid-β Protofibrils: A Molecular Dynamics Simulation Study.
    Zou Y, Qian Z, Chen Y, Qian H, Wei G, Zhang Q.
    ACS Chem Neurosci; 2019 Mar 20; 10(3):1585-1594. PubMed ID: 30605312
    [Abstract] [Full Text] [Related]

  • 16. Molecular Dynamics Simulations of Protein Aggregation: Protocols for Simulation Setup and Analysis with Markov State Models and Transition Networks.
    Samantray S, Schumann W, Illig AM, Carballo-Pacheco M, Paul A, Barz B, Strodel B.
    Methods Mol Biol; 2022 Mar 20; 2340():235-279. PubMed ID: 35167078
    [Abstract] [Full Text] [Related]

  • 17. Computer Simulations Aimed at Exploring Protein Aggregation and Dissociation.
    Nguyen PH, Derreumaux P.
    Methods Mol Biol; 2022 Mar 20; 2340():175-196. PubMed ID: 35167075
    [Abstract] [Full Text] [Related]

  • 18. Atomic-level characterization of the ensemble of the Aβ(1-42) monomer in water using unbiased molecular dynamics simulations and spectral algorithms.
    Sgourakis NG, Merced-Serrano M, Boutsidis C, Drineas P, Du Z, Wang C, Garcia AE.
    J Mol Biol; 2011 Jan 14; 405(2):570-83. PubMed ID: 21056574
    [Abstract] [Full Text] [Related]

  • 19. Replica sub-permutation method for molecular dynamics and monte carlo simulations.
    Yamauchi M, Okumura H.
    J Comput Chem; 2019 Dec 05; 40(31):2694-2711. PubMed ID: 31365132
    [Abstract] [Full Text] [Related]

  • 20. Study of the aggregation mechanism of polyglutamine peptides using replica exchange molecular dynamics simulations.
    Nakano M, Ebina K, Tanaka S.
    J Mol Model; 2013 Apr 05; 19(4):1627-39. PubMed ID: 23288093
    [Abstract] [Full Text] [Related]

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