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 *

144 related articles for article (PubMed ID: 34391359)

  • 1. An extended autoencoder model for reaction coordinate discovery in rare event molecular dynamics datasets.
    Frassek M; Arjun A; Bolhuis PG
    J Chem Phys; 2021 Aug; 155(6):064103. PubMed ID: 34391359
    [TBL] [Abstract][Full Text] [Related]  

  • 2. Protein Folding Free Energy Landscape along the Committor - the Optimal Folding Coordinate.
    Krivov SV
    J Chem Theory Comput; 2018 Jul; 14(7):3418-3427. PubMed ID: 29791148
    [TBL] [Abstract][Full Text] [Related]  

  • 3. Discovering Collective Variables of Molecular Transitions via Genetic Algorithms and Neural Networks.
    Hooft F; Pérez de Alba Ortíz A; Ensing B
    J Chem Theory Comput; 2021 Apr; 17(4):2294-2306. PubMed ID: 33662202
    [TBL] [Abstract][Full Text] [Related]  

  • 4. Discovering Reaction Pathways, Slow Variables, and Committor Probabilities with Machine Learning.
    Chen H; Roux B; Chipot C
    J Chem Theory Comput; 2023 Jul; 19(14):4414-4426. PubMed ID: 37224455
    [TBL] [Abstract][Full Text] [Related]  

  • 5. A deep autoencoder framework for discovery of metastable ensembles in biomacromolecules.
    Bandyopadhyay S; Mondal J
    J Chem Phys; 2021 Sep; 155(11):114106. PubMed ID: 34551528
    [TBL] [Abstract][Full Text] [Related]  

  • 6. Reaction coordinates and transition pathways of rare events via forward flux sampling.
    Borrero EE; Escobedo FA
    J Chem Phys; 2007 Oct; 127(16):164101. PubMed ID: 17979313
    [TBL] [Abstract][Full Text] [Related]  

  • 7. Nonlinear Reaction Coordinate of an Enzyme Catalyzed Proton Transfer Reaction.
    Paul TK; Taraphder S
    J Phys Chem B; 2022 Feb; 126(7):1413-1425. PubMed ID: 35138854
    [TBL] [Abstract][Full Text] [Related]  

  • 8. Reaction Coordinates and Mechanistic Hypothesis Tests.
    Peters B
    Annu Rev Phys Chem; 2016 May; 67():669-90. PubMed ID: 27090846
    [TBL] [Abstract][Full Text] [Related]  

  • 9. MLCV: Bridging Machine-Learning-Based Dimensionality Reduction and Free-Energy Calculation.
    Chen H; Liu H; Feng H; Fu H; Cai W; Shao X; Chipot C
    J Chem Inf Model; 2022 Jan; 62(1):1-8. PubMed ID: 34939790
    [TBL] [Abstract][Full Text] [Related]  

  • 10. An exploration of machine learning models for the determination of reaction coordinates associated with conformational transitions.
    Naleem N; Abreu CRA; Warmuz K; Tong M; Kirmizialtin S; Tuckerman ME
    J Chem Phys; 2023 Jul; 159(3):. PubMed ID: 37458344
    [TBL] [Abstract][Full Text] [Related]  

  • 11. Transition rate theory, spectral analysis, and reactive paths.
    Roux B
    J Chem Phys; 2022 Apr; 156(13):134111. PubMed ID: 35395906
    [TBL] [Abstract][Full Text] [Related]  

  • 12. Optimizing reaction coordinate by flux maximization in the transition path ensemble.
    Li W
    J Chem Phys; 2022 Feb; 156(5):054117. PubMed ID: 35135266
    [TBL] [Abstract][Full Text] [Related]  

  • 13. Learning reaction coordinates via cross-entropy minimization: Application to alanine dipeptide.
    Mori Y; Okazaki KI; Mori T; Kim K; Matubayasi N
    J Chem Phys; 2020 Aug; 153(5):054115. PubMed ID: 32770909
    [TBL] [Abstract][Full Text] [Related]  

  • 14. Nonlinear reaction coordinate analysis in the reweighted path ensemble.
    Lechner W; Rogal J; Juraszek J; Ensing B; Bolhuis PG
    J Chem Phys; 2010 Nov; 133(17):174110. PubMed ID: 21054009
    [TBL] [Abstract][Full Text] [Related]  

  • 15. Characterization of a dynamic string method for the construction of transition pathways in molecular reactions.
    Johnson ME; Hummer G
    J Phys Chem B; 2012 Jul; 116(29):8573-83. PubMed ID: 22616575
    [TBL] [Abstract][Full Text] [Related]  

  • 16. Autoencoders for dimensionality reduction in molecular dynamics: Collective variable dimension, biasing, and transition states.
    Belkacemi Z; Bianciotto M; Minoux H; Lelièvre T; Stoltz G; Gkeka P
    J Chem Phys; 2023 Jul; 159(2):. PubMed ID: 37431908
    [TBL] [Abstract][Full Text] [Related]  

  • 17. Perspective: Identification of collective variables and metastable states of protein dynamics.
    Sittel F; Stock G
    J Chem Phys; 2018 Oct; 149(15):150901. PubMed ID: 30342445
    [TBL] [Abstract][Full Text] [Related]  

  • 18. Identification of a multi-dimensional reaction coordinate for crystal nucleation in Ni
    Liang Y; Díaz Leines G; Drautz R; Rogal J
    J Chem Phys; 2020 Jun; 152(22):224504. PubMed ID: 32534529
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Nonparametric Analysis of Nonequilibrium Simulations.
    Krivov SV
    J Chem Theory Comput; 2021 Sep; 17(9):5466-5481. PubMed ID: 34464134
    [TBL] [Abstract][Full Text] [Related]  

  • 20. On committor functions in milestoning.
    Ji X; Wang R; Wang H; Liu W
    J Chem Phys; 2023 Dec; 159(24):. PubMed ID: 38153148
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 8.