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 *

222 related articles for article (PubMed ID: 34283604)

  • 1. Reaction Path-Force Matching in Collective Variables: Determining Ab Initio QM/MM Free Energy Profiles by Fitting Mean Force.
    Kim B; Snyder R; Nagaraju M; Zhou Y; Ojeda-May P; Keeton S; Hege M; Shao Y; Pu J
    J Chem Theory Comput; 2021 Aug; 17(8):4961-4980. PubMed ID: 34283604
    [TBL] [Abstract][Full Text] [Related]  

  • 2. Reaction Path Force Matching: A New Strategy of Fitting Specific Reaction Parameters for Semiempirical Methods in Combined QM/MM Simulations.
    Zhou Y; Pu J
    J Chem Theory Comput; 2014 Aug; 10(8):3038-54. PubMed ID: 26588275
    [TBL] [Abstract][Full Text] [Related]  

  • 3. Bridging semiempirical and ab initio QM/MM potentials by Gaussian process regression and its sparse variants for free energy simulation.
    Snyder R; Kim B; Pan X; Shao Y; Pu J
    J Chem Phys; 2023 Aug; 159(5):. PubMed ID: 37530109
    [TBL] [Abstract][Full Text] [Related]  

  • 4. Facilitating
    Snyder R; Kim B; Pan X; Shao Y; Pu J
    Phys Chem Chem Phys; 2022 Oct; 24(41):25134-25143. PubMed ID: 36222412
    [TBL] [Abstract][Full Text] [Related]  

  • 5. Doubly Polarized QM/MM with Machine Learning Chaperone Polarizability.
    Kim B; Shao Y; Pu J
    J Chem Theory Comput; 2021 Dec; 17(12):7682-7695. PubMed ID: 34723536
    [TBL] [Abstract][Full Text] [Related]  

  • 6. Accelerated computation of free energy profile at ab initio quantum mechanical/molecular mechanical accuracy via a semi-empirical reference potential. II. Recalibrating semi-empirical parameters with force matching.
    Pan X; Li P; Ho J; Pu J; Mei Y; Shao Y
    Phys Chem Chem Phys; 2019 Oct; 21(37):20595-20605. PubMed ID: 31508625
    [TBL] [Abstract][Full Text] [Related]  

  • 7. Toward Determining ATPase Mechanism in ABC Transporters: Development of the Reaction Path-Force Matching QM/MM Method.
    Zhou Y; Ojeda-May P; Nagaraju M; Pu J
    Methods Enzymol; 2016; 577():185-212. PubMed ID: 27498639
    [TBL] [Abstract][Full Text] [Related]  

  • 8. Machine-Learning-Assisted Free Energy Simulation of Solution-Phase and Enzyme Reactions.
    Pan X; Yang J; Van R; Epifanovsky E; Ho J; Huang J; Pu J; Mei Y; Nam K; Shao Y
    J Chem Theory Comput; 2021 Sep; 17(9):5745-5758. PubMed ID: 34468138
    [TBL] [Abstract][Full Text] [Related]  

  • 9. QM/MM Minimum Free Energy Path: Methodology and Application to Triosephosphate Isomerase.
    Hu H; Lu Z; Yang W
    J Chem Theory Comput; 2007 Mar; 3(2):390-406. PubMed ID: 19079734
    [TBL] [Abstract][Full Text] [Related]  

  • 10. Quantum mechanics/molecular mechanics minimum free-energy path for accurate reaction energetics in solution and enzymes: sequential sampling and optimization on the potential of mean force surface.
    Hu H; Lu Z; Parks JM; Burger SK; Yang W
    J Chem Phys; 2008 Jan; 128(3):034105. PubMed ID: 18205486
    [TBL] [Abstract][Full Text] [Related]  

  • 11. Accelerating
    Pan X; Van R; Epifanovsky E; Liu J; Pu J; Nam K; Shao Y
    J Phys Chem B; 2022 Jun; ():. PubMed ID: 35653199
    [TBL] [Abstract][Full Text] [Related]  

  • 12. Efficient Computation of Free Energy Surfaces of Diels⁻Alder Reactions in Explicit Solvent at Ab Initio QM/MM Level.
    Li P; Liu F; Jia X; Shao Y; Hu W; Zheng J; Mei Y
    Molecules; 2018 Sep; 23(10):. PubMed ID: 30274188
    [TBL] [Abstract][Full Text] [Related]  

  • 13. Reaction path potential for complex systems derived from combined ab initio quantum mechanical and molecular mechanical calculations.
    Lu Z; Yang W
    J Chem Phys; 2004 Jul; 121(1):89-100. PubMed ID: 15260525
    [TBL] [Abstract][Full Text] [Related]  

  • 14. AM1 Specific Reaction Parameters for Reactions of Hydroxide Ion with Halomethanes in Complex Environments: Development and Testing.
    Liang S; Roitberg AE
    J Chem Theory Comput; 2013 Oct; 9(10):4470-80. PubMed ID: 26589165
    [TBL] [Abstract][Full Text] [Related]  

  • 15. Combined QM/MM, Machine Learning Path Integral Approach to Compute Free Energy Profiles and Kinetic Isotope Effects in RNA Cleavage Reactions.
    Giese TJ; Zeng J; Ekesan Ş; York DM
    J Chem Theory Comput; 2022 Jul; 18(7):4304-4317. PubMed ID: 35709391
    [TBL] [Abstract][Full Text] [Related]  

  • 16. Comparison of linear-scaling semiempirical methods and combined quantum mechanical/molecular mechanical methods for enzymic reactions. II. An energy decomposition analysis.
    Titmuss SJ; Cummins PL; Rendell AP; Bliznyuk AA; Gready JE
    J Comput Chem; 2002 Nov; 23(14):1314-22. PubMed ID: 12214314
    [TBL] [Abstract][Full Text] [Related]  

  • 17. Quantifying free energy profiles of proton transfer reactions in solution and proteins by using a diabatic FDFT mapping.
    Xiang Y; Warshel A
    J Phys Chem B; 2008 Jan; 112(3):1007-15. PubMed ID: 18166038
    [TBL] [Abstract][Full Text] [Related]  

  • 18. Towards accurate ab initio QM/MM calculations of free-energy profiles of enzymatic reactions.
    Rosta E; Klähn M; Warshel A
    J Phys Chem B; 2006 Feb; 110(6):2934-41. PubMed ID: 16471904
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Computational Insights into Endo/Exo Selectivity of the Diels-Alder Reaction in Explicit Solvent at Ab Initio Quantum Mechanical/Molecular Mechanical Level.
    Li P; Liu F; Shao Y; Mei Y
    J Phys Chem B; 2019 Jun; 123(24):5131-5138. PubMed ID: 31140808
    [TBL] [Abstract][Full Text] [Related]  

  • 20. Acceleration of Ab Initio QM/MM Calculations under Periodic Boundary Conditions by Multiscale and Multiple Time Step Approaches.
    Nam K
    J Chem Theory Comput; 2014 Oct; 10(10):4175-83. PubMed ID: 26588116
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 12.