BIOMARKERS

Molecular Biopsy of Human Tumors

- a resource for Precision Medicine *

140 related articles for article (PubMed ID: 29529369)

  • 1. Transferable Neural Networks for Enhanced Sampling of Protein Dynamics.
    Sultan MM; Wayment-Steele HK; Pande VS
    J Chem Theory Comput; 2018 Apr; 14(4):1887-1894. PubMed ID: 29529369
    [TBL] [Abstract][Full Text] [Related]  

  • 2. 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]  

  • 3. 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]  

  • 4. Transfer Learning from Markov Models Leads to Efficient Sampling of Related Systems.
    Sultan MM; Pande VS
    J Phys Chem B; 2018 May; 122(21):5291-5299. PubMed ID: 28938073
    [TBL] [Abstract][Full Text] [Related]  

  • 5. Enhanced Conformational Sampling Using Replica Exchange with Collective-Variable Tempering.
    Gil-Ley A; Bussi G
    J Chem Theory Comput; 2015 Mar; 11(3):1077-85. PubMed ID: 25838811
    [TBL] [Abstract][Full Text] [Related]  

  • 6. Refining Collective Coordinates and Improving Free Energy Representation in Variational Enhanced Sampling.
    Yang YI; Parrinello M
    J Chem Theory Comput; 2018 Jun; 14(6):2889-2894. PubMed ID: 29715017
    [TBL] [Abstract][Full Text] [Related]  

  • 7. Deep learning path-like collective variable for enhanced sampling molecular dynamics.
    Fröhlking T; Bonati L; Rizzi V; Gervasio FL
    J Chem Phys; 2024 May; 160(17):. PubMed ID: 38748013
    [TBL] [Abstract][Full Text] [Related]  

  • 8. LINES: Log-Probability Estimation via Invertible Neural Networks for Enhanced Sampling.
    Odstrcil RE; Dutta P; Liu J
    J Chem Theory Comput; 2022 Oct; 18(10):6297-6309. PubMed ID: 36099438
    [TBL] [Abstract][Full Text] [Related]  

  • 9. Reinforced dynamics for enhanced sampling in large atomic and molecular systems.
    Zhang L; Wang H; E W
    J Chem Phys; 2018 Mar; 148(12):124113. PubMed ID: 29604808
    [TBL] [Abstract][Full Text] [Related]  

  • 10. A kernel-based approach to molecular conformation analysis.
    Klus S; Bittracher A; Schuster I; Schütte C
    J Chem Phys; 2018 Dec; 149(24):244109. PubMed ID: 30599717
    [TBL] [Abstract][Full Text] [Related]  

  • 11. Hierarchical Coupling of First-Principles Molecular Dynamics with Advanced Sampling Methods.
    Sevgen E; Giberti F; Sidky H; Whitmer JK; Galli G; Gygi F; de Pablo JJ
    J Chem Theory Comput; 2018 Jun; 14(6):2881-2888. PubMed ID: 29694787
    [TBL] [Abstract][Full Text] [Related]  

  • 12. Unfolding Hidden Barriers by Active Enhanced Sampling.
    Zhang J; Chen M
    Phys Rev Lett; 2018 Jul; 121(1):010601. PubMed ID: 30028174
    [TBL] [Abstract][Full Text] [Related]  

  • 13. 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]  

  • 14. Free Energy Reconstruction from Logarithmic Mean-Force Dynamics Using Multiple Nonequilibrium Trajectories.
    Morishita T; Yonezawa Y; Ito AM
    J Chem Theory Comput; 2017 Jul; 13(7):3106-3119. PubMed ID: 28602083
    [TBL] [Abstract][Full Text] [Related]  

  • 15. A convective replica-exchange method for sampling new energy basins.
    Spill YG; Bouvier G; Nilges M
    J Comput Chem; 2013 Jan; 34(2):132-40. PubMed ID: 22961200
    [TBL] [Abstract][Full Text] [Related]  

  • 16. Multiple pathways in conformational transitions of the alanine dipeptide: an application of dynamic importance sampling.
    Jang H; Woolf TB
    J Comput Chem; 2006 Aug; 27(11):1136-41. PubMed ID: 16721720
    [TBL] [Abstract][Full Text] [Related]  

  • 17. The temperature intervals with global exchange of replicas empirical accelerated sampling method: parameter sensitivity and extension to a complex molecular system.
    Li X; Latour RA
    J Comput Chem; 2011 Apr; 32(6):1091-100. PubMed ID: 20949510
    [TBL] [Abstract][Full Text] [Related]  

  • 18. Hamiltonian replica-permutation method and its applications to an alanine dipeptide and amyloid-β(29-42) peptides.
    Itoh SG; Okumura H
    J Comput Chem; 2013 Nov; 34(29):2493-7. PubMed ID: 23925979
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Water-mediated conformations of the alanine dipeptide as revealed by distributed umbrella sampling simulations, quantum mechanics based calculations, and experimental data.
    Cruz V; Ramos J; Martínez-Salazar J
    J Phys Chem B; 2011 Apr; 115(16):4880-6. PubMed ID: 21469661
    [TBL] [Abstract][Full Text] [Related]  

  • 20. The Allostery Landscape: Quantifying Thermodynamic Couplings in Biomolecular Systems.
    Cuendet MA; Weinstein H; LeVine MV
    J Chem Theory Comput; 2016 Dec; 12(12):5758-5767. PubMed ID: 27766843
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 7.