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 *

175 related articles for article (PubMed ID: 37787134)

  • 1. 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]  

  • 2. 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]  

  • 3. 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]  

  • 4. Building insightful, memory-enriched models to capture long-time biochemical processes from short-time simulations.
    Dominic AJ; Sayer T; Cao S; Markland TE; Huang X; Montoya-Castillo A
    Proc Natl Acad Sci U S A; 2023 Mar; 120(12):e2221048120. PubMed ID: 36920924
    [TBL] [Abstract][Full Text] [Related]  

  • 5. 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]  

  • 6. Generalized master equation for charge transport in a molecular junction: Exact memory kernels and their high order expansion.
    Dan X; Xu M; Yan Y; Shi Q
    J Chem Phys; 2022 Apr; 156(13):134114. PubMed ID: 35395901
    [TBL] [Abstract][Full Text] [Related]  

  • 7. Role of bacterial RNA polymerase gate opening dynamics in DNA loading and antibiotics inhibition elucidated by quasi-Markov State Model.
    Unarta IC; Cao S; Kubo S; Wang W; Cheung PP; Gao X; Takada S; Huang X
    Proc Natl Acad Sci U S A; 2021 Apr; 118(17):. PubMed ID: 33883282
    [TBL] [Abstract][Full Text] [Related]  

  • 8. Theoretical study of charge carrier transport in organic molecular crystals using the Nakajima-Zwanzig-Mori generalized master equation.
    Yan Y; Xu M; Liu Y; Shi Q
    J Chem Phys; 2019 Jun; 150(23):234101. PubMed ID: 31228885
    [TBL] [Abstract][Full Text] [Related]  

  • 9. 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]  

  • 10. 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]  

  • 11. A deep learning approach to the measurement of long-lived memory kernels from generalized Langevin dynamics.
    Kerr Winter M; Pihlajamaa I; Debets VE; Janssen LMC
    J Chem Phys; 2023 Jun; 158(24):. PubMed ID: 37366311
    [TBL] [Abstract][Full Text] [Related]  

  • 12. Persistent topology and metastable state in conformational dynamics.
    Chang HW; Bacallado S; Pande VS; Carlsson GE
    PLoS One; 2013; 8(4):e58699. PubMed ID: 23565139
    [TBL] [Abstract][Full Text] [Related]  

  • 13. 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]  

  • 14. Convergence of high order memory kernels in the Nakajima-Zwanzig generalized master equation and rate constants: Case study of the spin-boson model.
    Xu M; Yan Y; Liu Y; Shi Q
    J Chem Phys; 2018 Apr; 148(16):164101. PubMed ID: 29716231
    [TBL] [Abstract][Full Text] [Related]  

  • 15. Resummed memory kernels in generalized system-bath master equations.
    Mavros MG; Van Voorhis T
    J Chem Phys; 2014 Aug; 141(5):054112. PubMed ID: 25106575
    [TBL] [Abstract][Full Text] [Related]  

  • 16. 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]  

  • 17. The multi-dimensional generalized Langevin equation for conformational motion of proteins.
    Lee HS; Ahn SH; Darve EF
    J Chem Phys; 2019 May; 150(17):174113. PubMed ID: 31067888
    [TBL] [Abstract][Full Text] [Related]  

  • 18. 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]  

  • 19. Exploring Biomolecular Conformational Dynamics with Polarizable Force Field AMOEBA and Enhanced Sampling Method Milestoning.
    Yang X; Liu C; Ren P
    J Chem Theory Comput; 2024 May; 20(10):4065-4075. PubMed ID: 38742922
    [TBL] [Abstract][Full Text] [Related]  

  • 20. A Gauss-Newton method for iterative optimization of memory kernels for generalized Langevin thermostats in coarse-grained molecular dynamics simulations.
    Klippenstein V; Wolf N; van der Vegt NFA
    J Chem Phys; 2024 May; 160(20):. PubMed ID: 38804493
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 9.