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 *

127 related articles for article (PubMed ID: 39085770)

  • 1. Multiple Parameter Replica Exchange Gaussian Accelerated Molecular Dynamics for Enhanced Sampling and Free Energy Calculation of Biomolecular Systems.
    Hasse T; Huang YM
    J Chem Theory Comput; 2024 Aug; 20(15):6485-6499. PubMed ID: 39085770
    [TBL] [Abstract][Full Text] [Related]  

  • 2. Replica Exchange Gaussian Accelerated Molecular Dynamics: Improved Enhanced Sampling and Free Energy Calculation.
    Huang YM; McCammon JA; Miao Y
    J Chem Theory Comput; 2018 Apr; 14(4):1853-1864. PubMed ID: 29489349
    [TBL] [Abstract][Full Text] [Related]  

  • 3. Gaussian accelerated molecular dynamics (GaMD): principles and applications.
    Wang J; Arantes PR; Bhattarai A; Hsu RV; Pawnikar S; Huang YM; Palermo G; Miao Y
    Wiley Interdiscip Rev Comput Mol Sci; 2021; 11(5):. PubMed ID: 34899998
    [TBL] [Abstract][Full Text] [Related]  

  • 4. Replica-Exchange Umbrella Sampling Combined with Gaussian Accelerated Molecular Dynamics for Free-Energy Calculation of Biomolecules.
    Oshima H; Re S; Sugita Y
    J Chem Theory Comput; 2019 Oct; 15(10):5199-5208. PubMed ID: 31539245
    [TBL] [Abstract][Full Text] [Related]  

  • 5. Acceleration of biomolecular kinetics in Gaussian accelerated molecular dynamics.
    Miao Y
    J Chem Phys; 2018 Aug; 149(7):072308. PubMed ID: 30134710
    [TBL] [Abstract][Full Text] [Related]  

  • 6. Gaussian Accelerated Molecular Dynamics in NAMD.
    Pang YT; Miao Y; Wang Y; McCammon JA
    J Chem Theory Comput; 2017 Jan; 13(1):9-19. PubMed ID: 28034310
    [TBL] [Abstract][Full Text] [Related]  

  • 7. Gaussian Accelerated Molecular Dynamics: Unconstrained Enhanced Sampling and Free Energy Calculation.
    Miao Y; Feher VA; McCammon JA
    J Chem Theory Comput; 2015 Aug; 11(8):3584-3595. PubMed ID: 26300708
    [TBL] [Abstract][Full Text] [Related]  

  • 8. Gaussian accelerated molecular dynamics for elucidation of drug pathways.
    Bhattarai A; Miao Y
    Expert Opin Drug Discov; 2018 Nov; 13(11):1055-1065. PubMed ID: 30371112
    [TBL] [Abstract][Full Text] [Related]  

  • 9. Gaussian Accelerated Molecular Dynamics: Theory, Implementation, and Applications.
    Miao Y; McCammon JA
    Annu Rep Comput Chem; 2017; 13():231-278. PubMed ID: 29720925
    [TBL] [Abstract][Full Text] [Related]  

  • 10. Sigmoid Accelerated Molecular Dynamics: An Efficient Enhanced Sampling Method for Biosystems.
    Zhao Y; Zhang J; Zhang H; Gu S; Deng Y; Tu Y; Hou T; Kang Y
    J Phys Chem Lett; 2023 Feb; 14(4):1103-1112. PubMed ID: 36700836
    [TBL] [Abstract][Full Text] [Related]  

  • 11. Replica-Exchange Methods for Biomolecular Simulations.
    Sugita Y; Kamiya M; Oshima H; Re S
    Methods Mol Biol; 2019; 2022():155-177. PubMed ID: 31396903
    [TBL] [Abstract][Full Text] [Related]  

  • 12. Flexible Gaussian Accelerated Molecular Dynamics to Enhance Biological Sampling.
    Gracia Carmona O; Oostenbrink C
    J Chem Theory Comput; 2023 Sep; 19(18):6521-6531. PubMed ID: 37649349
    [TBL] [Abstract][Full Text] [Related]  

  • 13. Ligand Binding Pathways and Conformational Transitions of the HIV Protease.
    Miao Y; Huang YM; Walker RC; McCammon JA; Chang CA
    Biochemistry; 2018 Mar; 57(9):1533-1541. PubMed ID: 29394043
    [TBL] [Abstract][Full Text] [Related]  

  • 14. Gaussian Accelerated Molecular Dynamics in OpenMM.
    Copeland MM; Do HN; Votapka L; Joshi K; Wang J; Amaro RE; Miao Y
    J Phys Chem B; 2022 Aug; 126(31):5810-5820. PubMed ID: 35895977
    [TBL] [Abstract][Full Text] [Related]  

  • 15. When MELD Meets GaMD: Accelerating Biomolecular Landscape Exploration.
    Caparotta M; Perez A
    J Chem Theory Comput; 2023 Dec; 19(23):8743-8750. PubMed ID: 38039424
    [TBL] [Abstract][Full Text] [Related]  

  • 16. Population based reweighting of scaled molecular dynamics.
    Sinko W; Miao Y; de Oliveira CA; McCammon JA
    J Phys Chem B; 2013 Oct; 117(42):12759-68. PubMed ID: 23721224
    [TBL] [Abstract][Full Text] [Related]  

  • 17. Peptide Gaussian accelerated molecular dynamics (Pep-GaMD): Enhanced sampling and free energy and kinetics calculations of peptide binding.
    Wang J; Miao Y
    J Chem Phys; 2020 Oct; 153(15):154109. PubMed ID: 33092378
    [TBL] [Abstract][Full Text] [Related]  

  • 18. An Efficient Gaussian-Accelerated Molecular Dynamics (GaMD) Multilevel Enhanced Sampling Strategy: Application to Polarizable Force Fields Simulations of Large Biological Systems.
    Célerse F; Inizan TJ; Lagardère L; Adjoua O; Monmarché P; Miao Y; Derat E; Piquemal JP
    J Chem Theory Comput; 2022 Feb; 18(2):968-977. PubMed ID: 35080892
    [TBL] [Abstract][Full Text] [Related]  

  • 19. GLOW: A Workflow Integrating Gaussian-Accelerated Molecular Dynamics and Deep Learning for Free Energy Profiling.
    Do HN; Wang J; Bhattarai A; Miao Y
    J Chem Theory Comput; 2022 Mar; 18(3):1423-1436. PubMed ID: 35200019
    [TBL] [Abstract][Full Text] [Related]  

  • 20. Boosting the conformational sampling by combining replica exchange with solute tempering and well-sliced metadynamics.
    Kapakayala AB; Nair NN
    J Comput Chem; 2021 Dec; 42(31):2233-2240. PubMed ID: 34585768
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 7.