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Journal Abstract Search

590 related items for PubMed ID: 17120231

  • 1. Enhanced sampling of peptide and protein conformations using replica exchange simulations with a peptide backbone biasing-potential.
    Kannan S, Zacharias M.
    Proteins; 2007 Feb 15; 66(3):697-706. PubMed ID: 17120231
    [Abstract] [Full Text] [Related]

  • 2. Folding simulations of Trp-cage mini protein in explicit solvent using biasing potential replica-exchange molecular dynamics simulations.
    Kannan S, Zacharias M.
    Proteins; 2009 Aug 01; 76(2):448-60. PubMed ID: 19173315
    [Abstract] [Full Text] [Related]

  • 3. Simulated annealing coupled replica exchange molecular dynamics--an efficient conformational sampling method.
    Kannan S, Zacharias M.
    J Struct Biol; 2009 Jun 01; 166(3):288-94. PubMed ID: 19272454
    [Abstract] [Full Text] [Related]

  • 4. Application of biasing-potential replica-exchange simulations for loop modeling and refinement of proteins in explicit solvent.
    Kannan S, Zacharias M.
    Proteins; 2010 Oct 01; 78(13):2809-19. PubMed ID: 20635348
    [Abstract] [Full Text] [Related]

  • 5. Enhanced conformational sampling of nucleic acids by a new Hamiltonian replica exchange molecular dynamics approach.
    Curuksu J, Zacharias M.
    J Chem Phys; 2009 Mar 14; 130(10):104110. PubMed ID: 19292526
    [Abstract] [Full Text] [Related]

  • 6. Convergence and sampling efficiency in replica exchange simulations of peptide folding in explicit solvent.
    Periole X, Mark AE.
    J Chem Phys; 2007 Jan 07; 126(1):014903. PubMed ID: 17212515
    [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 15; 35(2):150-8. PubMed ID: 24318649
    [Abstract] [Full Text] [Related]

  • 8. Simulated-tempering replica-exchange method for the multidimensional version.
    Mitsutake A.
    J Chem Phys; 2009 Sep 07; 131(9):094105. PubMed ID: 19739847
    [Abstract] [Full Text] [Related]

  • 9. An improved replica-exchange sampling method: temperature intervals with global energy reassignment.
    Li X, O'Brien CP, Collier G, Vellore NA, Wang F, Latour RA, Bruce DA, Stuart SJ.
    J Chem Phys; 2007 Oct 28; 127(16):164116. PubMed ID: 17979328
    [Abstract] [Full Text] [Related]

  • 10. Dissociation aided and side chain sampling enhanced Hamiltonian replica exchange.
    Mu Y.
    J Chem Phys; 2009 Apr 28; 130(16):164107. PubMed ID: 19405561
    [Abstract] [Full Text] [Related]

  • 11. Estimating kinetic rates from accelerated molecular dynamics simulations: alanine dipeptide in explicit solvent as a case study.
    de Oliveira CA, Hamelberg D, McCammon JA.
    J Chem Phys; 2007 Nov 07; 127(17):175105. PubMed ID: 17994855
    [Abstract] [Full Text] [Related]

  • 12. Efficient evaluation of sampling quality of molecular dynamics simulations by clustering of dihedral torsion angles and Sammon mapping.
    Frickenhaus S, Kannan S, Zacharias M.
    J Comput Chem; 2009 Feb 07; 30(3):479-92. PubMed ID: 18680215
    [Abstract] [Full Text] [Related]

  • 13. Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations.
    Mackerell AD, Feig M, Brooks CL.
    J Comput Chem; 2004 Aug 07; 25(11):1400-15. PubMed ID: 15185334
    [Abstract] [Full Text] [Related]

  • 14. Reordering hydrogen bonds using hamiltonian replica exchange enhances sampling of conformational changes in biomolecular systems.
    Vreede J, Wolf MG, de Leeuw SW, Bolhuis PG.
    J Phys Chem B; 2009 May 07; 113(18):6484-94. PubMed ID: 19358572
    [Abstract] [Full Text] [Related]

  • 15. Reversible folding simulation by hybrid Hamiltonian replica exchange.
    Xu W, Lai T, Yang Y, Mu Y.
    J Chem Phys; 2008 May 07; 128(17):175105. PubMed ID: 18465944
    [Abstract] [Full Text] [Related]

  • 16. Structure and energy landscape of a photoswitchable peptide: a replica exchange molecular dynamics study.
    Nguyen PH, Mu Y, Stock G.
    Proteins; 2005 Aug 15; 60(3):485-94. PubMed ID: 15977160
    [Abstract] [Full Text] [Related]

  • 17. Combining Elastic Network Analysis and Molecular Dynamics Simulations by Hamiltonian Replica Exchange.
    Zacharias M.
    J Chem Theory Comput; 2008 Mar 15; 4(3):477-87. PubMed ID: 26620788
    [Abstract] [Full Text] [Related]

  • 18. Replica exchange simulation method using temperature and solvent viscosity.
    Nguyen PH.
    J Chem Phys; 2010 Apr 14; 132(14):144109. PubMed ID: 20405987
    [Abstract] [Full Text] [Related]

  • 19. Replica exchange with dynamical scaling.
    Rick SW.
    J Chem Phys; 2007 Feb 07; 126(5):054102. PubMed ID: 17302469
    [Abstract] [Full Text] [Related]

  • 20. Multiple scaling replica exchange for the conformational sampling of biomolecules in explicit water.
    Kamberaj H, van der Vaart A.
    J Chem Phys; 2007 Dec 21; 127(23):234102. PubMed ID: 18154370
    [Abstract] [Full Text] [Related]

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