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Journal Abstract Search

425 related items for PubMed ID: 24484442

  • 21. Accuracy of Protein Embedding Potentials: An Analysis in Terms of Electrostatic Potentials.
    Olsen JM, List NH, Kristensen K, Kongsted J.
    J Chem Theory Comput; 2015 Apr 14; 11(4):1832-42. PubMed ID: 26574389
    [Abstract] [Full Text] [Related]

  • 22. Cytochrome P450CAM enzymatic catalysis cycle: a quantum mechanics/molecular mechanics study.
    Guallar V, Friesner RA.
    J Am Chem Soc; 2004 Jul 14; 126(27):8501-8. PubMed ID: 15238007
    [Abstract] [Full Text] [Related]

  • 23. Effect of the QM Size, Basis Set, and Polarization on QM/MM Interaction Energy Decomposition Analysis.
    Pérez-Barcia Á, Cárdenas G, Nogueira JJ, Mandado M.
    J Chem Inf Model; 2023 Feb 13; 63(3):882-897. PubMed ID: 36661314
    [Abstract] [Full Text] [Related]

  • 24. Electron transfer in the P450cam/PDX complex. The QM/MM e-pathway.
    Wallrapp F, Masone D, Guallar V.
    J Phys Chem A; 2008 Dec 18; 112(50):12989-94. PubMed ID: 18823106
    [Abstract] [Full Text] [Related]

  • 25. QM/MM study of the second proton transfer in the catalytic cycle of the D251N mutant of cytochrome P450cam.
    Altarsha M, Wang D, Benighaus T, Kumar D, Thiel W.
    J Phys Chem B; 2009 Jul 16; 113(28):9577-88. PubMed ID: 19537775
    [Abstract] [Full Text] [Related]

  • 26. A Polarizable QM/MM Model That Combines the State-Averaged CASSCF and AMOEBA Force Field for Photoreactions in Proteins.
    Song C, Wang LP.
    J Chem Theory Comput; 2024 Aug 13; 20(15):6632-6651. PubMed ID: 39088696
    [Abstract] [Full Text] [Related]

  • 27. Solvent Boundary Potentials for Hybrid QM/MM Computations Using Classical Drude Oscillators: A Fully Polarizable Model.
    Boulanger E, Thiel W.
    J Chem Theory Comput; 2012 Nov 13; 8(11):4527-38. PubMed ID: 26605612
    [Abstract] [Full Text] [Related]

  • 28. How do substrates enter and products exit the buried active site of cytochrome P450cam? 2. Steered molecular dynamics and adiabatic mapping of substrate pathways.
    Lüdemann SK, Lounnas V, Wade RC.
    J Mol Biol; 2000 Nov 10; 303(5):813-30. PubMed ID: 11061977
    [Abstract] [Full Text] [Related]

  • 29. The Quality of the Embedding Potential Is Decisive for Minimal Quantum Region Size in Embedding Calculations: The Case of the Green Fluorescent Protein.
    Nåbo LJ, Olsen JMH, Martínez TJ, Kongsted J.
    J Chem Theory Comput; 2017 Dec 12; 13(12):6230-6236. PubMed ID: 29099597
    [Abstract] [Full Text] [Related]

  • 30. Chromophore-protein coupling beyond nonpolarizable models: understanding absorption in green fluorescent protein.
    Daday C, Curutchet C, Sinicropi A, Mennucci B, Filippi C.
    J Chem Theory Comput; 2015 Oct 13; 11(10):4825-39. PubMed ID: 26574271
    [Abstract] [Full Text] [Related]

  • 31. 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
    [Abstract] [Full Text] [Related]

  • 32. Combined QM/MM calculations of active-site vibrations in binding process of P450cam to putidaredoxin.
    Freindorf M, Shao Y, Kong J, Furlani TR.
    J Inorg Biochem; 2008 Mar 21; 102(3):427-32. PubMed ID: 18180042
    [Abstract] [Full Text] [Related]

  • 33. Self-Consistent Polarization of the Boundary in the Redistributed Charge and Dipole Scheme for Combined Quantum-Mechanical and Molecular-Mechanical Calculations.
    Zhang Y, Lin H, Truhlar DG.
    J Chem Theory Comput; 2007 Jul 21; 3(4):1378-98. PubMed ID: 26633210
    [Abstract] [Full Text] [Related]

  • 34. Curvature correction for microiterative optimizations with QM/MM electronic embedding.
    Rokob TA, Rulíšek L.
    J Comput Chem; 2012 May 05; 33(12):1197-206. PubMed ID: 22344958
    [Abstract] [Full Text] [Related]

  • 35. Conformational simulations of aqueous solvated alpha-conotoxin GI and its single disulfide analogues using a polarizable force field model.
    Jiang N, Ma J.
    J Phys Chem A; 2008 Oct 09; 112(40):9854-67. PubMed ID: 18788721
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  • 36. QuanPol: a full spectrum and seamless QM/MM program.
    Thellamurege NM, Si D, Cui F, Zhu H, Lai R, Li H.
    J Comput Chem; 2013 Dec 15; 34(32):2816-33. PubMed ID: 24122765
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  • 37. QM:QM electronic embedding using Mulliken atomic charges: energies and analytic gradients in an ONIOM framework.
    Hratchian HP, Parandekar PV, Raghavachari K, Frisch MJ, Vreven T.
    J Chem Phys; 2008 Jan 21; 128(3):034107. PubMed ID: 18205488
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  • 38. Quantum mechanical/molecular mechanical calculated reactivity networks reveal how cytochrome P450cam and Its T252A mutant select their oxidation pathways.
    Wang B, Li C, Dubey KD, Shaik S.
    J Am Chem Soc; 2015 Jun 17; 137(23):7379-90. PubMed ID: 26011529
    [Abstract] [Full Text] [Related]

  • 39. Thermodynamics calculation of protein-ligand interactions by QM/MM polarizable charge parameters.
    Wang J, Shao Q, Cossins BP, Shi J, Chen K, Zhu W.
    J Biomol Struct Dyn; 2016 Jun 17; 34(1):163-76. PubMed ID: 25761118
    [Abstract] [Full Text] [Related]

  • 40. 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 28; 129(12):125105. PubMed ID: 19045066
    [Abstract] [Full Text] [Related]

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