BIOMARKERS

Molecular Biopsy of Human Tumors

- a resource for Precision Medicine *

184 related articles for article (PubMed ID: 33662202)

  • 1. 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]  

  • 2. 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]  

  • 3. 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]  

  • 4. The Adaptive Path Collective Variable: A Versatile Biasing Approach to Compute the Average Transition Path and Free Energy of Molecular Transitions.
    Pérez de Alba Ortíz A; Vreede J; Ensing B
    Methods Mol Biol; 2019; 2022():255-290. PubMed ID: 31396907
    [TBL] [Abstract][Full Text] [Related]  

  • 5. Explaining reaction coordinates of alanine dipeptide isomerization obtained from deep neural networks using Explainable Artificial Intelligence (XAI).
    Kikutsuji T; Mori Y; Okazaki KI; Mori T; Kim K; Matubayasi N
    J Chem Phys; 2022 Apr; 156(15):154108. PubMed ID: 35459300
    [TBL] [Abstract][Full Text] [Related]  

  • 6. DeepCV: A Deep Learning Framework for Blind Search of Collective Variables in Expanded Configurational Space.
    Ketkaew R; Luber S
    J Chem Inf Model; 2022 Dec; 62(24):6352-6364. PubMed ID: 36445176
    [TBL] [Abstract][Full Text] [Related]  

  • 7. 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]  

  • 8. 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]  

  • 9. Finding transition pathways using the string method with swarms of trajectories.
    Pan AC; Sezer D; Roux B
    J Phys Chem B; 2008 Mar; 112(11):3432-40. PubMed ID: 18290641
    [TBL] [Abstract][Full Text] [Related]  

  • 10. Modeling and enhanced sampling of molecular systems with smooth and nonlinear data-driven collective variables.
    Hashemian B; Millán D; Arroyo M
    J Chem Phys; 2013 Dec; 139(21):214101. PubMed ID: 24320358
    [TBL] [Abstract][Full Text] [Related]  

  • 11. 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]  

  • 12. Automated design of collective variables using supervised machine learning.
    Sultan MM; Pande VS
    J Chem Phys; 2018 Sep; 149(9):094106. PubMed ID: 30195289
    [TBL] [Abstract][Full Text] [Related]  

  • 13. Collective variable discovery and enhanced sampling using autoencoders: Innovations in network architecture and error function design.
    Chen W; Tan AR; Ferguson AL
    J Chem Phys; 2018 Aug; 149(7):072312. PubMed ID: 30134681
    [TBL] [Abstract][Full Text] [Related]  

  • 14. Automatic method for identifying reaction coordinates in complex systems.
    Ma A; Dinner AR
    J Phys Chem B; 2005 Apr; 109(14):6769-79. PubMed ID: 16851762
    [TBL] [Abstract][Full Text] [Related]  

  • 15. 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]  

  • 16. Collective Variable-Based Enhanced Sampling: From Human Learning to Machine Learning.
    Fu H; Bian H; Shao X; Cai W
    J Phys Chem Lett; 2024 Feb; 15(6):1774-1783. PubMed ID: 38329095
    [TBL] [Abstract][Full Text] [Related]  

  • 17. Nonlinear discovery of slow molecular modes using state-free reversible VAMPnets.
    Chen W; Sidky H; Ferguson AL
    J Chem Phys; 2019 Jun; 150(21):214114. PubMed ID: 31176319
    [TBL] [Abstract][Full Text] [Related]  

  • 18. Transition pathways in complex systems: Application of the finite-temperature string method to the alanine dipeptide.
    Ren W; Vanden-Eijnden E; Maragakis P; E W
    J Chem Phys; 2005 Oct; 123(13):134109. PubMed ID: 16223277
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Computing committors via Mahalanobis diffusion maps with enhanced sampling data.
    Evans L; Cameron MK; Tiwary P
    J Chem Phys; 2022 Dec; 157(21):214107. PubMed ID: 36511548
    [TBL] [Abstract][Full Text] [Related]  

  • 20. Metadynamics in essential coordinates: free energy simulation of conformational changes.
    Spiwok V; Lipovová P; Králová B
    J Phys Chem B; 2007 Mar; 111(12):3073-6. PubMed ID: 17388445
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 10.