BIOMARKERS

Molecular Biopsy of Human Tumors

- a resource for Precision Medicine *

291 related articles for article (PubMed ID: 26596615)

  • 1. Efficient Conformational Sampling in Explicit Solvent Using a Hybrid Replica Exchange Molecular Dynamics Method.
    Chaudhury S; Olson MA; Tawa G; Wallqvist A; Lee MS
    J Chem Theory Comput; 2012 Feb; 8(2):677-87. PubMed ID: 26596615
    [TBL] [Abstract][Full Text] [Related]  

  • 2. Improved Efficiency of Replica Exchange Simulations through Use of a Hybrid Explicit/Implicit Solvation Model.
    Okur A; Wickstrom L; Layten M; Geney R; Song K; Hornak V; Simmerling C
    J Chem Theory Comput; 2006 Mar; 2(2):420-33. PubMed ID: 26626529
    [TBL] [Abstract][Full Text] [Related]  

  • 3. Evaluation of Salt Bridge Structure and Energetics in Peptides Using Explicit, Implicit, and Hybrid Solvation Models.
    Okur A; Wickstrom L; Simmerling C
    J Chem Theory Comput; 2008 Mar; 4(3):488-98. PubMed ID: 26620789
    [TBL] [Abstract][Full Text] [Related]  

  • 4. Increasing the sampling efficiency of protein conformational transition using velocity-scaling optimized hybrid explicit/implicit solvent REMD simulation.
    Yu Y; Wang J; Shao Q; Shi J; Zhu W
    J Chem Phys; 2015 Mar; 142(12):125105. PubMed ID: 25833612
    [TBL] [Abstract][Full Text] [Related]  

  • 5. Free energy landscape of protein folding in water: explicit vs. implicit solvent.
    Zhou R
    Proteins; 2003 Nov; 53(2):148-61. PubMed ID: 14517967
    [TBL] [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; 126(1):014903. PubMed ID: 17212515
    [TBL] [Abstract][Full Text] [Related]  

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

  • 8. TIGER2 with solvent energy averaging (TIGER2A): An accelerated sampling method for large molecular systems with explicit representation of solvent.
    Li X; Snyder JA; Stuart SJ; Latour RA
    J Chem Phys; 2015 Oct; 143(14):144105. PubMed ID: 26472361
    [TBL] [Abstract][Full Text] [Related]  

  • 9. Improving the replica-exchange molecular-dynamics method for efficient sampling in the temperature space.
    Chen C; Xiao Y; Huang Y
    Phys Rev E Stat Nonlin Soft Matter Phys; 2015 May; 91(5):052708. PubMed ID: 26066200
    [TBL] [Abstract][Full Text] [Related]  

  • 10. 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; 123(28):5995-6006. PubMed ID: 31265293
    [TBL] [Abstract][Full Text] [Related]  

  • 11. 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]  

  • 12. Can a continuum solvent model reproduce the free energy landscape of a beta -hairpin folding in water?
    Zhou R; Berne BJ
    Proc Natl Acad Sci U S A; 2002 Oct; 99(20):12777-82. PubMed ID: 12242327
    [TBL] [Abstract][Full Text] [Related]  

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

  • 14. 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]  

  • 15. Walking freely in the energy and temperature space by the modified replica exchange molecular dynamics method.
    Chen C; Huang Y
    J Comput Chem; 2016 Jun; 37(17):1565-75. PubMed ID: 27059441
    [TBL] [Abstract][Full Text] [Related]  

  • 16. Exploring the protein folding free energy landscape: coupling replica exchange method with P3ME/RESPA algorithm.
    Zhou R
    J Mol Graph Model; 2004 May; 22(5):451-63. PubMed ID: 15099840
    [TBL] [Abstract][Full Text] [Related]  

  • 17. Flexible selection of the solute region in replica exchange with solute tempering: Application to protein-folding simulations.
    Kamiya M; Sugita Y
    J Chem Phys; 2018 Aug; 149(7):072304. PubMed ID: 30134668
    [TBL] [Abstract][Full Text] [Related]  

  • 18. 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]  

  • 19. Connecting free energy surfaces in implicit and explicit solvent: an efficient method to compute conformational and solvation free energies.
    Deng N; Zhang BW; Levy RM
    J Chem Theory Comput; 2015 Jun; 11(6):2868-78. PubMed ID: 26236174
    [TBL] [Abstract][Full Text] [Related]  

  • 20. Does Replica Exchange with Solute Tempering Efficiently Sample Aβ Peptide Conformational Ensembles?
    Smith AK; Lockhart C; Klimov DK
    J Chem Theory Comput; 2016 Oct; 12(10):5201-5214. PubMed ID: 27560127
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 15.