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354 related items for PubMed ID: 19079734

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  • 2. 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 21; 128(3):034105. PubMed ID: 18205486
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  • 6. Parallel iterative reaction path optimization in ab initio quantum mechanical/molecular mechanical modeling of enzyme reactions.
    Liu H, Lu Z, Cisneros GA, Yang W.
    J Chem Phys; 2004 Jul 08; 121(2):697-706. PubMed ID: 15260596
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  • 7. Molecular Dynamics Simulations with Quantum Mechanics/Molecular Mechanics and Adaptive Neural Networks.
    Shen L, Yang W.
    J Chem Theory Comput; 2018 Mar 13; 14(3):1442-1455. PubMed ID: 29438614
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  • 8. 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 16; 110(6):2934-41. PubMed ID: 16471904
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  • 9. Multiscale Quantum Mechanics/Molecular Mechanics Simulations with Neural Networks.
    Shen L, Wu J, Yang W.
    J Chem Theory Comput; 2016 Oct 11; 12(10):4934-4946. PubMed ID: 27552235
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  • 11. 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 24; 112(3):1007-15. PubMed ID: 18166038
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  • 12. 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 10; 17(8):4961-4980. PubMed ID: 34283604
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  • 13. Hybrid Quantum Mechanics/Molecular Mechanics Solvation Scheme for Computing Free Energies of Reactions at Metal-Water Interfaces.
    Faheem M, Heyden A.
    J Chem Theory Comput; 2014 Aug 12; 10(8):3354-68. PubMed ID: 26588304
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  • 14. 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 07; 159(5):. PubMed ID: 37530109
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  • 15. Elucidating solvent contributions to solution reactions with ab initio QM/MM methods.
    Hu H, Yang W.
    J Phys Chem B; 2010 Mar 04; 114(8):2755-9. PubMed ID: 20121225
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  • 18. Minimum Free Energy Pathways of Reactive Processes with Nudged Elastic Bands.
    Semelak JA, Zeida A, Foglia NO, Estrin DA.
    J Chem Theory Comput; 2023 Sep 26; 19(18):6273-6293. PubMed ID: 37647166
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  • 19. Facilitating ab initio QM/MM free energy simulations by Gaussian process regression with derivative observations.
    Snyder R, Kim B, Pan X, Shao Y, Pu J.
    Phys Chem Chem Phys; 2022 Oct 27; 24(41):25134-25143. PubMed ID: 36222412
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  • 20. Development and application of ab initio QM/MM methods for mechanistic simulation of reactions in solution and in enzymes.
    Hu H, Yang W.
    Theochem; 2009 Mar 30; 898(1-3):17-30. PubMed ID: 24146439
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