These tools will no longer be maintained as of December 31, 2024. Archived website can be found here. PubMed4Hh GitHub repository can be found here. Contact NLM Customer Service if you have questions.


BIOMARKERS

Molecular Biopsy of Human Tumors

- a resource for Precision Medicine *

192 related articles for article (PubMed ID: 28088161)

  • 1. Efficient free energy calculations by combining two complementary tempering sampling methods.
    Xie L; Shen L; Chen ZN; Yang M
    J Chem Phys; 2017 Jan; 146(2):024103. PubMed ID: 28088161
    [TBL] [Abstract][Full Text] [Related]  

  • 2. Combine umbrella sampling with integrated tempering method for efficient and accurate calculation of free energy changes of complex energy surface.
    Yang M; Yang L; Gao Y; Hu H
    J Chem Phys; 2014 Jul; 141(4):044108. PubMed ID: 25084882
    [TBL] [Abstract][Full Text] [Related]  

  • 3. Simultaneous escaping of explicit and hidden free energy barriers: application of the orthogonal space random walk strategy in generalized ensemble based conformational sampling.
    Zheng L; Chen M; Yang W
    J Chem Phys; 2009 Jun; 130(23):234105. PubMed ID: 19548709
    [TBL] [Abstract][Full Text] [Related]  

  • 4. Efficient sampling over rough energy landscapes with high barriers: A combination of metadynamics with integrated tempering sampling.
    Yang YI; Zhang J; Che X; Yang L; Gao YQ
    J Chem Phys; 2016 Mar; 144(9):094105. PubMed ID: 26957155
    [TBL] [Abstract][Full Text] [Related]  

  • 5. Temperature-Accelerated Sampling and Amplified Collective Motion with Adiabatic Reweighting to Obtain Canonical Distributions and Ensemble Averages.
    Hu Y; Hong W; Shi Y; Liu H
    J Chem Theory Comput; 2012 Oct; 8(10):3777-92. PubMed ID: 26593019
    [TBL] [Abstract][Full Text] [Related]  

  • 6. A selective integrated tempering method.
    Yang L; Qin Gao Y
    J Chem Phys; 2009 Dec; 131(21):214109. PubMed ID: 19968339
    [TBL] [Abstract][Full Text] [Related]  

  • 7. Optimizing String Method's Reproducibility Using Generalized Solute Tempering Replica Exchange.
    Shrivastav G; Abrams CF
    J Phys Chem B; 2021 Jun; 125(24):6609-6616. PubMed ID: 34110824
    [TBL] [Abstract][Full Text] [Related]  

  • 8. Comparison between integrated and parallel tempering methods in enhanced sampling simulations.
    Yang L; Shao Q; Gao YQ
    J Chem Phys; 2009 Mar; 130(12):124111. PubMed ID: 19334812
    [TBL] [Abstract][Full Text] [Related]  

  • 9. Efficient and direct generation of multidimensional free energy surfaces via adiabatic dynamics without coordinate transformations.
    Abrams JB; Tuckerman ME
    J Phys Chem B; 2008 Dec; 112(49):15742-57. PubMed ID: 19367870
    [TBL] [Abstract][Full Text] [Related]  

  • 10. Single-sweep methods for free energy calculations.
    Maragliano L; Vanden-Eijnden E
    J Chem Phys; 2008 May; 128(18):184110. PubMed ID: 18532802
    [TBL] [Abstract][Full Text] [Related]  

  • 11. Determining Protein Folding Pathway and Associated Energetics through Partitioned Integrated-Tempering-Sampling Simulation.
    Shao Q; Shi J; Zhu W
    J Chem Theory Comput; 2017 Mar; 13(3):1229-1243. PubMed ID: 28121433
    [TBL] [Abstract][Full Text] [Related]  

  • 12. Free Energy Calculations using a Swarm-Enhanced Sampling Molecular Dynamics Approach.
    Burusco KK; Bruce NJ; Alibay I; Bryce RA
    Chemphyschem; 2015 Oct; 16(15):3233-41. PubMed ID: 26418190
    [TBL] [Abstract][Full Text] [Related]  

  • 13. Free-energy analyses of a proton transfer reaction by simulated-tempering umbrella sampling and first-principles molecular dynamics simulations.
    Mori Y; Okamoto Y
    Phys Rev E Stat Nonlin Soft Matter Phys; 2013 Feb; 87(2):023301. PubMed ID: 23496633
    [TBL] [Abstract][Full Text] [Related]  

  • 14. Free energy and hidden barriers of the β-sheet structure of prion protein.
    Paz SA; Abrams CF
    J Chem Theory Comput; 2015 Oct; 11(10):5024-34. PubMed ID: 26574287
    [TBL] [Abstract][Full Text] [Related]  

  • 15. Enhanced ligand sampling for relative protein-ligand binding free energy calculations.
    Kaus JW; McCammon JA
    J Phys Chem B; 2015 May; 119(20):6190-7. PubMed ID: 25906170
    [TBL] [Abstract][Full Text] [Related]  

  • 16. Enhanced sampling and free energy calculations for protein simulations.
    Liao Q
    Prog Mol Biol Transl Sci; 2020; 170():177-213. PubMed ID: 32145945
    [TBL] [Abstract][Full Text] [Related]  

  • 17. Direct determination of reaction paths and stationary points on potential of mean force surfaces.
    Li G; Cui Q
    J Mol Graph Model; 2005 Oct; 24(2):82-93. PubMed ID: 16005650
    [TBL] [Abstract][Full Text] [Related]  

  • 18. Towards fast, rigorous and efficient conformational sampling of biomolecules: Advances in accelerated molecular dynamics.
    Doshi U; Hamelberg D
    Biochim Biophys Acta; 2015 May; 1850(5):878-888. PubMed ID: 25153688
    [TBL] [Abstract][Full Text] [Related]  

  • 19. On-the-Fly Specifications of Reaction Coordinates in Parallel Cascade Selection Molecular Dynamics Accelerate Conformational Transitions of Proteins.
    Harada R; Shigeta Y
    J Chem Theory Comput; 2018 Jun; 14(6):3332-3341. PubMed ID: 29727581
    [TBL] [Abstract][Full Text] [Related]  

  • 20. Enhancing pairwise state-transition weights: A new weighting scheme in simulated tempering that can minimize transition time between a pair of conformational states.
    Qiao Q; Zhang HD; Huang X
    J Chem Phys; 2016 Apr; 144(15):154107. PubMed ID: 27389209
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 10.