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 *

181 related articles for article (PubMed ID: 34985469)

  • 1. RPnet: a reverse-projection-based neural network for coarse-graining metastable conformational states for protein dynamics.
    Gu H; Wang W; Cao S; Unarta IC; Yao Y; Sheong FK; Huang X
    Phys Chem Chem Phys; 2022 Jan; 24(3):1462-1474. PubMed ID: 34985469
    [TBL] [Abstract][Full Text] [Related]  

  • 2. An efficient Bayesian kinetic lumping algorithm to identify metastable conformational states via Gibbs sampling.
    Wang W; Liang T; Sheong FK; Fan X; Huang X
    J Chem Phys; 2018 Aug; 149(7):072337. PubMed ID: 30134698
    [TBL] [Abstract][Full Text] [Related]  

  • 3. Hierarchical Nyström methods for constructing Markov state models for conformational dynamics.
    Yao Y; Cui RZ; Bowman GR; Silva DA; Sun J; Huang X
    J Chem Phys; 2013 May; 138(17):174106. PubMed ID: 23656113
    [TBL] [Abstract][Full Text] [Related]  

  • 4. On the advantages of exploiting memory in Markov state models for biomolecular dynamics.
    Cao S; Montoya-Castillo A; Wang W; Markland TE; Huang X
    J Chem Phys; 2020 Jul; 153(1):014105. PubMed ID: 32640825
    [TBL] [Abstract][Full Text] [Related]  

  • 5. Markov state models from hierarchical density-based assignment.
    Mitxelena I; López X; de Sancho D
    J Chem Phys; 2021 Aug; 155(5):054102. PubMed ID: 34364321
    [TBL] [Abstract][Full Text] [Related]  

  • 6. Conformational analysis of replica exchange MD: Temperature-dependent Markov networks for FF amyloid peptides.
    Narayan B; Herbert C; Yuan Y; Rodriguez BJ; Brooks BR; Buchete NV
    J Chem Phys; 2018 Aug; 149(7):072323. PubMed ID: 30134732
    [TBL] [Abstract][Full Text] [Related]  

  • 7. Application of Markov State Models to simulate long timescale dynamics of biological macromolecules.
    Da LT; Sheong FK; Silva DA; Huang X
    Adv Exp Med Biol; 2014; 805():29-66. PubMed ID: 24446356
    [TBL] [Abstract][Full Text] [Related]  

  • 8. Information Bottleneck Approach for Markov Model Construction.
    Wang D; Qiu Y; Beyerle ER; Huang X; Tiwary P
    J Chem Theory Comput; 2024 Jun; 20(12):5352-5367. PubMed ID: 38859575
    [TBL] [Abstract][Full Text] [Related]  

  • 9. Tutorial on how to build non-Markovian dynamic models from molecular dynamics simulations for studying protein conformational changes.
    Wu Y; Cao S; Qiu Y; Huang X
    J Chem Phys; 2024 Mar; 160(12):. PubMed ID: 38516972
    [TBL] [Abstract][Full Text] [Related]  

  • 10. Dynamic neutron scattering from conformational dynamics. II. Application using molecular dynamics simulation and Markov modeling.
    Yi Z; Lindner B; Prinz JH; Noé F; Smith JC
    J Chem Phys; 2013 Nov; 139(17):175102. PubMed ID: 24206335
    [TBL] [Abstract][Full Text] [Related]  

  • 11. Constructing Kinetic Network Models to Elucidate Mechanisms of Functional Conformational Changes of Enzymes and Their Recognition with Ligands.
    Zhang L; Jiang H; Sheong FK; Pardo-Avila F; Cheung PP; Huang X
    Methods Enzymol; 2016; 578():343-71. PubMed ID: 27497174
    [TBL] [Abstract][Full Text] [Related]  

  • 12. Macromolecular crowding: chemistry and physics meet biology (Ascona, Switzerland, 10-14 June 2012).
    Foffi G; Pastore A; Piazza F; Temussi PA
    Phys Biol; 2013 Aug; 10(4):040301. PubMed ID: 23912807
    [TBL] [Abstract][Full Text] [Related]  

  • 13. An Efficient Path Classification Algorithm Based on Variational Autoencoder to Identify Metastable Path Channels for Complex Conformational Changes.
    Qiu Y; O'Connor MS; Xue M; Liu B; Huang X
    J Chem Theory Comput; 2023 Jul; 19(14):4728-4742. PubMed ID: 37382437
    [TBL] [Abstract][Full Text] [Related]  

  • 14. 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]  

  • 15. Integrative generalized master equation: A method to study long-timescale biomolecular dynamics via the integrals of memory kernels.
    Cao S; Qiu Y; Kalin ML; Huang X
    J Chem Phys; 2023 Oct; 159(13):. PubMed ID: 37787134
    [TBL] [Abstract][Full Text] [Related]  

  • 16. Automatic state partitioning for multibody systems (APM): an efficient algorithm for constructing Markov state models to elucidate conformational dynamics of multibody systems.
    Sheong FK; Silva DA; Meng L; Zhao Y; Huang X
    J Chem Theory Comput; 2015 Jan; 11(1):17-27. PubMed ID: 26574199
    [TBL] [Abstract][Full Text] [Related]  

  • 17. A Minimum Variance Clustering Approach Produces Robust and Interpretable Coarse-Grained Models.
    Husic BE; McKiernan KA; Wayment-Steele HK; Sultan MM; Pande VS
    J Chem Theory Comput; 2018 Feb; 14(2):1071-1082. PubMed ID: 29253336
    [TBL] [Abstract][Full Text] [Related]  

  • 18. Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics.
    Chodera JD; Singhal N; Pande VS; Dill KA; Swope WC
    J Chem Phys; 2007 Apr; 126(15):155101. PubMed ID: 17461665
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Dimensional reduction of Markov state models from renormalization group theory.
    Orioli S; Faccioli P
    J Chem Phys; 2016 Sep; 145(12):124120. PubMed ID: 27782633
    [TBL] [Abstract][Full Text] [Related]  

  • 20. Long-time methods for molecular dynamics simulations: Markov State Models and Milestoning.
    Narayan B; Yuan Y; Fathizadeh A; Elber R; Buchete NV
    Prog Mol Biol Transl Sci; 2020; 170():215-237. PubMed ID: 32145946
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 10.