BIOMARKERS

Molecular Biopsy of Human Tumors

- a resource for Precision Medicine *

359 related articles for article (PubMed ID: 26626529)

  • 1. 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]  

  • 2. 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]  

  • 3. 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]  

  • 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. Secondary structure bias in generalized Born solvent models: comparison of conformational ensembles and free energy of solvent polarization from explicit and implicit solvation.
    Roe DR; Okur A; Wickstrom L; Hornak V; Simmerling C
    J Phys Chem B; 2007 Feb; 111(7):1846-57. PubMed ID: 17256983
    [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. 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]  

  • 8. 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]  

  • 9. Conformational space search of Neuromedin C using replica exchange molecular dynamics and molecular dynamics.
    Sharma P; Singh P; Bisetty K; Rodriguez A; Perez JJ
    J Pept Sci; 2011 Mar; 17(3):174-83. PubMed ID: 20878681
    [TBL] [Abstract][Full Text] [Related]  

  • 10. Improving Convergence of Replica-Exchange Simulations through Coupling to a High-Temperature Structure Reservoir.
    Okur A; Roe DR; Cui G; Hornak V; Simmerling C
    J Chem Theory Comput; 2007 Mar; 3(2):557-68. PubMed ID: 26637035
    [TBL] [Abstract][Full Text] [Related]  

  • 11. 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]  

  • 12. 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]  

  • 13. Discrimination between native and intentionally misfolded conformations of proteins: ES/IS, a new method for calculating conformational free energy that uses both dynamics simulations with an explicit solvent and an implicit solvent continuum model.
    Vorobjev YN; Almagro JC; Hermans J
    Proteins; 1998 Sep; 32(4):399-413. PubMed ID: 9726412
    [TBL] [Abstract][Full Text] [Related]  

  • 14. 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]  

  • 15. 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]  

  • 16. Convergence of replica exchange molecular dynamics.
    Zhang W; Wu C; Duan Y
    J Chem Phys; 2005 Oct; 123(15):154105. PubMed ID: 16252940
    [TBL] [Abstract][Full Text] [Related]  

  • 17. Ensuring Mixing Efficiency of Replica-Exchange Molecular Dynamics Simulations.
    Abraham MJ; Gready JE
    J Chem Theory Comput; 2008 Jul; 4(7):1119-28. PubMed ID: 26636365
    [TBL] [Abstract][Full Text] [Related]  

  • 18. Exploring the energy landscape of protein folding using replica-exchange and conventional molecular dynamics simulations.
    Beck DA; White GW; Daggett V
    J Struct Biol; 2007 Mar; 157(3):514-23. PubMed ID: 17113307
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Molecular dynamics simulations of peptides and proteins with a continuum electrostatic model based on screened Coulomb potentials.
    Hassan SA; Mehler EL; Zhang D; Weinstein H
    Proteins; 2003 Apr; 51(1):109-25. PubMed ID: 12596268
    [TBL] [Abstract][Full Text] [Related]  

  • 20. Replica exchange molecular dynamics simulations of coarse-grained proteins in implicit solvent.
    Chebaro Y; Dong X; Laghaei R; Derreumaux P; Mousseau N
    J Phys Chem B; 2009 Jan; 113(1):267-74. PubMed ID: 19067549
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 18.