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569 related items for PubMed ID: 18161687

  • 1. Dynamic structures of phosphodiesterase-5 active site by combined molecular dynamics simulations and hybrid quantum mechanical/molecular mechanical calculations.
    Xiong Y, Lu HT, Zhan CG.
    J Comput Chem; 2008 Jun; 29(8):1259-67. PubMed ID: 18161687
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  • 2. Characterization of a catalytic ligand bridging metal ions in phosphodiesterases 4 and 5 by molecular dynamics simulations and hybrid quantum mechanical/molecular mechanical calculations.
    Xiong Y, Lu HT, Li Y, Yang GF, Zhan CG.
    Biophys J; 2006 Sep 01; 91(5):1858-67. PubMed ID: 16912214
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  • 3. Active site dynamics and combined quantum mechanics/molecular mechanics (QM/MM) modelling of a HIV-1 reverse transcriptase/DNA/dTTP complex.
    Rungrotmongkol T, Mulholland AJ, Hannongbua S.
    J Mol Graph Model; 2007 Jul 01; 26(1):1-13. PubMed ID: 17046299
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  • 4. Redistributed charge and dipole schemes for combined quantum mechanical and molecular mechanical calculations.
    Lin H, Truhlar DG.
    J Phys Chem A; 2005 May 05; 109(17):3991-4004. PubMed ID: 16833721
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  • 5. pKa calculations in solution and proteins with QM/MM free energy perturbation simulations: a quantitative test of QM/MM protocols.
    Riccardi D, Schaefer P, Cui Q.
    J Phys Chem B; 2005 Sep 22; 109(37):17715-33. PubMed ID: 16853267
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  • 11. Characterization of the active site of DNA polymerase beta by molecular dynamics and quantum chemical calculation.
    Rittenhouse RC, Apostoluk WK, Miller JH, Straatsma TP.
    Proteins; 2003 Nov 15; 53(3):667-82. PubMed ID: 14579358
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  • 14. Coordination number of zinc ions in the phosphotriesterase active site by molecular dynamics and quantum mechanics.
    Koca J, Zhan CG, Rittenhouse RC, Ornstein RL.
    J Comput Chem; 2003 Feb 15; 24(3):368-78. PubMed ID: 12548728
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  • 17. Importance of polarization in quantum mechanics/molecular mechanics descriptions of electronic excited states: NaI(H2O)n photodissociation dynamics as a case study.
    Koch DM, Peslherbe GH.
    J Phys Chem B; 2008 Jan 17; 112(2):636-49. PubMed ID: 18183959
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  • 18. Simulations of liquid ammonia based on the combined quantum mechanical/molecular mechanical (QM/MM) approach.
    Tongraar A, Kerdcharoen T, Hannongbua S.
    J Phys Chem A; 2006 Apr 13; 110(14):4924-9. PubMed ID: 16599463
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  • 19. Comprehensive molecular mechanics model for oxidized type I copper proteins: active site structures, strain energies, and entatic bulging.
    Deeth RJ.
    Inorg Chem; 2007 May 28; 46(11):4492-503. PubMed ID: 17461575
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  • 20. A multicore QM/MM approach for the geometry optimization of chromophore aggregate in protein.
    Kiyota Y, Hasegawa JY, Fujimoto K, Swerts B, Nakatsuji H.
    J Comput Chem; 2009 Jun 28; 30(8):1351-9. PubMed ID: 19009605
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