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Journal Abstract Search

172 related items for PubMed ID: 21133348

  • 1. Quantum mechanics/molecular mechanics strategies for docking pose refinement: distinguishing between binders and decoys in cytochrome C peroxidase.
    Burger SK, Thompson DC, Ayers PW.
    J Chem Inf Model; 2011 Jan 24; 51(1):93-101. PubMed ID: 21133348
    [Abstract] [Full Text] [Related]

  • 2. Protein/ligand binding free energies calculated with quantum mechanics/molecular mechanics.
    Gräter F, Schwarzl SM, Dejaegere A, Fischer S, Smith JC.
    J Phys Chem B; 2005 May 26; 109(20):10474-83. PubMed ID: 16852269
    [Abstract] [Full Text] [Related]

  • 3. A comparative study of trypsin specificity based on QM/MM molecular dynamics simulation and QM/MM GBSA calculation.
    Chen J, Wang J, Zhang Q, Chen K, Zhu W.
    J Biomol Struct Dyn; 2015 May 26; 33(12):2606-18. PubMed ID: 25562613
    [Abstract] [Full Text] [Related]

  • 4. Quantum refinement of protein structures: implementation and application to the red fluorescent protein DsRed.M1.
    Hsiao YW, Sanchez-Garcia E, Doerr M, Thiel W.
    J Phys Chem B; 2010 Nov 25; 114(46):15413-23. PubMed ID: 20977248
    [Abstract] [Full Text] [Related]

  • 5. The MM2QM tool for combining docking, molecular dynamics, molecular mechanics, and quantum mechanics.
    Nowosielski M, Hoffmann M, Kuron A, Korycka-Machala M, Dziadek J.
    J Comput Chem; 2013 Apr 05; 34(9):750-6. PubMed ID: 23233437
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  • 6. Insights into docking and scoring neuronal alpha4beta2 nicotinic receptor agonists using molecular dynamics simulations and QM/MM calculations.
    Sgrignani J, Bonaccini C, Grazioso G, Chioccioli M, Cavalli A, Gratteri P.
    J Comput Chem; 2009 Nov 30; 30(15):2443-54. PubMed ID: 19360794
    [Abstract] [Full Text] [Related]

  • 7. 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 30; 26(1):1-13. PubMed ID: 17046299
    [Abstract] [Full Text] [Related]

  • 8. Refinement of protein crystal structures using energy restraints derived from linear-scaling quantum mechanics.
    Yu N, Yennawar HP, Merz KM.
    Acta Crystallogr D Biol Crystallogr; 2005 Mar 30; 61(Pt 3):322-32. PubMed ID: 15735343
    [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 21; 128(3):034105. PubMed ID: 18205486
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  • 14. Construction and assessment of models of CYP2E1: predictions of metabolism from docking, molecular dynamics, and density functional theoretical calculations.
    Park JY, Harris D.
    J Med Chem; 2003 Apr 24; 46(9):1645-60. PubMed ID: 12699383
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  • 16. QM/MM studies of structural and energetic properties of the far-red fluorescent protein HcRed.
    Sun Q, Doerr M, Li Z, Smith SC, Thiel W.
    Phys Chem Chem Phys; 2010 Mar 14; 12(10):2450-8. PubMed ID: 20449359
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  • 20. Rapid refinement of protein interfaces incorporating solvation: application to the docking problem.
    Jackson RM, Gabb HA, Sternberg MJ.
    J Mol Biol; 1998 Feb 13; 276(1):265-85. PubMed ID: 9514726
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