BIOMARKERS

Molecular Biopsy of Human Tumors

- a resource for Precision Medicine *

170 related articles for article (PubMed ID: 37943896)

  • 1. Free Energy Profile Decomposition Analysis for QM/MM Simulations of Enzymatic Reactions.
    Pan X; Van R; Pu J; Nam K; Mao Y; Shao Y
    J Chem Theory Comput; 2023 Nov; 19(22):8234-8244. PubMed ID: 37943896
    [TBL] [Abstract][Full Text] [Related]  

  • 2. 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]  

  • 3. 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]  

  • 4. 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]  

  • 5. Probing protein environment in an enzymatic process: All-electron quantum chemical analysis combined with ab initio quantum mechanical/molecular mechanical modeling of chorismate mutase.
    Ishida T
    J Chem Phys; 2008 Sep; 129(12):125105. PubMed ID: 19045066
    [TBL] [Abstract][Full Text] [Related]  

  • 6. 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]  

  • 7. 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]  

  • 8. 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]  

  • 9. 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]  

  • 10. Elucidating solvent contributions to solution reactions with ab initio QM/MM methods.
    Hu H; Yang W
    J Phys Chem B; 2010 Mar; 114(8):2755-9. PubMed ID: 20121225
    [TBL] [Abstract][Full Text] [Related]  

  • 11. 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]  

  • 12. 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]  

  • 13. Transition state stabilization and substrate strain in enzyme catalysis: ab initio QM/MM modelling of the chorismate mutase reaction.
    Ranaghan KE; Ridder L; Szefczyk B; Sokalski WA; Hermann JC; Mulholland AJ
    Org Biomol Chem; 2004 Apr; 2(7):968-80. PubMed ID: 15034619
    [TBL] [Abstract][Full Text] [Related]  

  • 14. 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]  

  • 15. 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]  

  • 16. Accelerated Computation of Free Energy Profile at ab Initio Quantum Mechanical/Molecular Mechanics Accuracy via a Semi-Empirical Reference Potential. I. Weighted Thermodynamics Perturbation.
    Li P; Jia X; Pan X; Shao Y; Mei Y
    J Chem Theory Comput; 2018 Nov; 14(11):5583-5596. PubMed ID: 30336015
    [TBL] [Abstract][Full Text] [Related]  

  • 17. Paradynamics: an effective and reliable model for ab initio QM/MM free-energy calculations and related tasks.
    Plotnikov NV; Kamerlin SC; Warshel A
    J Phys Chem B; 2011 Jun; 115(24):7950-62. PubMed ID: 21618985
    [TBL] [Abstract][Full Text] [Related]  

  • 18. Advances in quantum and molecular mechanical (QM/MM) simulations for organic and enzymatic reactions.
    Acevedo O; Jorgensen WL
    Acc Chem Res; 2010 Jan; 43(1):142-51. PubMed ID: 19728702
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Importance of MM Polarization in QM/MM Studies of Enzymatic Reactions: Assessment of the QM/MM Drude Oscillator Model.
    Ganguly A; Boulanger E; Thiel W
    J Chem Theory Comput; 2017 Jun; 13(6):2954-2961. PubMed ID: 28437096
    [TBL] [Abstract][Full Text] [Related]  

  • 20. Multiple-steering QM-MM calculation of the free energy profile in chorismate mutase.
    Crespo A; Martí MA; Estrin DA; Roitberg AE
    J Am Chem Soc; 2005 May; 127(19):6940-1. PubMed ID: 15884923
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 9.