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223 related items for PubMed ID: 26178083

  • 1. Communication: Multiple atomistic force fields in a single enhanced sampling simulation.
    Hoang Viet M, Derreumaux P, Nguyen PH.
    J Chem Phys; 2015 Jul 14; 143(2):021101. PubMed ID: 26178083
    [Abstract] [Full Text] [Related]

  • 2. Folding Atomistic Proteins in Explicit Solvent Using Simulated Tempering.
    Zhang T, Nguyen PH, Nasica-Labouze J, Mu Y, Derreumaux P.
    J Phys Chem B; 2015 Jun 11; 119(23):6941-51. PubMed ID: 25985144
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  • 3. Computational study of the free energy landscape of the miniprotein CLN025 in explicit and implicit solvent.
    Rodriguez A, Mokoema P, Corcho F, Bisetty K, Perez JJ.
    J Phys Chem B; 2011 Feb 17; 115(6):1440-9. PubMed ID: 21254763
    [Abstract] [Full Text] [Related]

  • 4. 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]

  • 5. 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
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  • 6. Multiscale investigation of chemical interference in proteins.
    Samiotakis A, Homouz D, Cheung MS.
    J Chem Phys; 2010 May 07; 132(17):175101. PubMed ID: 20459186
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  • 7. Simulated Tempering Distributed Replica Sampling, Virtual Replica Exchange, and Other Generalized-Ensemble Methods for Conformational Sampling.
    Rauscher S, Neale C, Pomès R.
    J Chem Theory Comput; 2009 Oct 13; 5(10):2640-62. PubMed ID: 26631779
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  • 8. Enhanced sampling algorithms.
    Mitsutake A, Mori Y, Okamoto Y.
    Methods Mol Biol; 2013 Oct 13; 924():153-95. PubMed ID: 23034749
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  • 9. 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 13; 82(12):3410-9. PubMed ID: 25243707
    [Abstract] [Full Text] [Related]

  • 10. Boosting the conformational sampling by combining replica exchange with solute tempering and well-sliced metadynamics.
    Kapakayala AB, Nair NN.
    J Comput Chem; 2021 Dec 05; 42(31):2233-2240. PubMed ID: 34585768
    [Abstract] [Full Text] [Related]

  • 11. 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]

  • 12. Re-Balancing Replica Exchange with Solute Tempering for Sampling Dynamic Protein Conformations.
    Zhang Y, Liu X, Chen J.
    J Chem Theory Comput; 2023 Mar 14; 19(5):1602-1614. PubMed ID: 36791464
    [Abstract] [Full Text] [Related]

  • 13. Continuous Tempering Molecular Dynamics: A Deterministic Approach to Simulated Tempering.
    Lenner N, Mathias G.
    J Chem Theory Comput; 2016 Feb 09; 12(2):486-98. PubMed ID: 26760910
    [Abstract] [Full Text] [Related]

  • 14. Replica-Based Protein Structure Sampling Methods II: Advanced Hybrid Solvent TIGER2hs.
    Geist N, Kulke M, Schulig L, Link A, Langel W.
    J Phys Chem B; 2019 Jul 18; 123(28):5995-6006. PubMed ID: 31265293
    [Abstract] [Full Text] [Related]

  • 15. Experimental verification of force fields for molecular dynamics simulations using Gly-Pro-Gly-Gly.
    Aliev AE, Courtier-Murias D.
    J Phys Chem B; 2010 Sep 30; 114(38):12358-75. PubMed ID: 20825228
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  • 16. Replica-Exchange Methods for Biomolecular Simulations.
    Sugita Y, Kamiya M, Oshima H, Re S.
    Methods Mol Biol; 2019 Sep 30; 2022():155-177. PubMed ID: 31396903
    [Abstract] [Full Text] [Related]

  • 17. Transform and relax sampling for highly anisotropic systems: application to protein domain motion and folding.
    Kitao A.
    J Chem Phys; 2011 Jul 28; 135(4):045101. PubMed ID: 21806159
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  • 18. Assessing equilibration and convergence in biomolecular simulations.
    Smith LJ, Daura X, van Gunsteren WF.
    Proteins; 2002 Aug 15; 48(3):487-96. PubMed ID: 12112673
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  • 19. A selective integrated tempering method.
    Yang L, Qin Gao Y.
    J Chem Phys; 2009 Dec 07; 131(21):214109. PubMed ID: 19968339
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  • 20. Temperature and pressure denaturation of chignolin: folding and unfolding simulation by multibaric-multithermal molecular dynamics method.
    Okumura H.
    Proteins; 2012 Oct 07; 80(10):2397-416. PubMed ID: 22641605
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