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Journal Abstract Search

206 related items for PubMed ID: 25838811

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  • 4. 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
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  • 5. Replica state exchange metadynamics for improving the convergence of free energy estimates.
    Galvelis R, Sugita Y.
    J Comput Chem; 2015 Jul 15; 36(19):1446-55. PubMed ID: 25990969
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  • 6. 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 05; 34(29):2493-7. PubMed ID: 23925979
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  • 7. Continuous metadynamics in essential coordinates as a tool for free energy modelling of conformational changes.
    Spiwok V, Králová B, Tvaroska I.
    J Mol Model; 2008 Nov 05; 14(11):995-1002. PubMed ID: 18633653
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  • 8. Reconstructing the equilibrium Boltzmann distribution from well-tempered metadynamics.
    Bonomi M, Barducci A, Parrinello M.
    J Comput Chem; 2009 Aug 05; 30(11):1615-21. PubMed ID: 19421997
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  • 10. Metadynamics as a tool for mapping the conformational and free-energy space of peptides--the alanine dipeptide case study.
    Vymetal J, Vondrásek J.
    J Phys Chem B; 2010 Apr 29; 114(16):5632-42. PubMed ID: 20361773
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  • 13. 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 27; 102(39):13749-54. PubMed ID: 16172406
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  • 15. 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
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  • 17. Enhanced exchange algorithm without detailed balance condition for replica exchange method.
    Kondo HX, Taiji M.
    J Chem Phys; 2013 Jun 28; 138(24):244113. PubMed ID: 23822233
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  • 18. 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 09; 13(5):1934-1942. PubMed ID: 28399363
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  • 19. Minimum free energy pathways and free energy profiles for conformational transitions based on atomistic molecular dynamics simulations.
    van der Vaart A, Karplus M.
    J Chem Phys; 2007 Apr 28; 126(16):164106. PubMed ID: 17477588
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  • 20. 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 07; 132(13):134105. PubMed ID: 20387919
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