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Journal Abstract Search

256 related items for PubMed ID: 16098779

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  • 4. Calculation of absolute ligand binding free energy to a ribosome-targeting protein as a function of solvent model.
    Lee MS, Olson MA.
    J Phys Chem B; 2008 Oct 23; 112(42):13411-7. PubMed ID: 18821791
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  • 5. Application of the frozen atom approximation to the GB/SA continuum model for solvation free energy.
    Guvench O, Weiser J, Shenkin P, Kolossváry I, Still WC.
    J Comput Chem; 2002 Jan 30; 23(2):214-21. PubMed ID: 11924735
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  • 6. Postprocessing of docked protein-ligand complexes using implicit solvation models.
    Lindström A, Edvinsson L, Johansson A, Andersson CD, Andersson IE, Raubacher F, Linusson A.
    J Chem Inf Model; 2011 Feb 28; 51(2):267-82. PubMed ID: 21309544
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  • 7. Combining docking, scoring and molecular field analyses to probe influenza neuraminidase-ligand interactions.
    Abu Hammad AM, Afifi FU, Taha MO.
    J Mol Graph Model; 2007 Sep 28; 26(2):443-56. PubMed ID: 17360207
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  • 8. Accurate prediction of protonation state as a prerequisite for reliable MM-PB(GB)SA binding free energy calculations of HIV-1 protease inhibitors.
    Wittayanarakul K, Hannongbua S, Feig M.
    J Comput Chem; 2008 Apr 15; 29(5):673-85. PubMed ID: 17849388
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  • 9. Modeling loop reorganization free energies of acetylcholinesterase: a comparison of explicit and implicit solvent models.
    Olson MA.
    Proteins; 2004 Dec 01; 57(4):645-50. PubMed ID: 15481087
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  • 10. FURSMASA: a new approach to rapid scoring functions that uses a MD-averaged potential energy grid and a solvent-accessible surface area term with parameters GA fit to experimental data.
    Pearlman DA, Rao BG, Charifson P.
    Proteins; 2008 May 15; 71(3):1519-38. PubMed ID: 18300249
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  • 11. AGBNP: an analytic implicit solvent model suitable for molecular dynamics simulations and high-resolution modeling.
    Gallicchio E, Levy RM.
    J Comput Chem; 2004 Mar 15; 25(4):479-99. PubMed ID: 14735568
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  • 12. Molecular dynamics and free energy analysis of neuraminidase-ligand interactions.
    Bonnet P, Bryce RA.
    Protein Sci; 2004 Apr 15; 13(4):946-57. PubMed ID: 15044728
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  • 13. Investigation of neuraminidase-substrate recognition using molecular dynamics and free energy calculations.
    Masukawa KM, Kollman PA, Kuntz ID.
    J Med Chem; 2003 Dec 18; 46(26):5628-37. PubMed ID: 14667217
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  • 14. Continuum solvation models in the linear interaction energy method.
    Carlsson J, Andér M, Nervall M, Aqvist J.
    J Phys Chem B; 2006 Jun 22; 110(24):12034-41. PubMed ID: 16800513
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  • 15. Prediction of ligand-receptor binding thermodynamics by free energy force field three-dimensional quantitative structure-activity relationship analysis: applications to a set of glucose analogue inhibitors of glycogen phosphorylase.
    Venkatarangan P, Hopfinger AJ.
    J Med Chem; 1999 Jun 17; 42(12):2169-79. PubMed ID: 10377222
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  • 16. Validation of an automated procedure for the prediction of relative free energies of binding on a set of aldose reductase inhibitors.
    Ferrari AM, Degliesposti G, Sgobba M, Rastelli G.
    Bioorg Med Chem; 2007 Dec 15; 15(24):7865-77. PubMed ID: 17870536
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  • 17. Absolute free energies of binding of peptide analogs to the HIV-1 protease from molecular dynamics simulations.
    Bartels C, Widmer A, Ehrhardt C.
    J Comput Chem; 2005 Sep 15; 26(12):1294-305. PubMed ID: 15981257
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  • 18. pH dependence of binding reactions from free energy simulations and macroscopic continuum electrostatic calculations: application to 2'GMP/3'GMP binding to ribonuclease T1 and implications for catalysis.
    MacKerell AD, Sommer MS, Karplus M.
    J Mol Biol; 1995 Apr 07; 247(4):774-807. PubMed ID: 7723031
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  • 19. Binding interaction analysis of the active site and its inhibitors for neuraminidase (N1 subtype) of human influenza virus by the integration of molecular docking, FMO calculation and 3D-QSAR CoMFA modeling.
    Zhang Q, Yang J, Liang K, Feng L, Li S, Wan J, Xu X, Yang G, Liu D, Yang S.
    J Chem Inf Model; 2008 Sep 07; 48(9):1802-12. PubMed ID: 18707092
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  • 20. Comparison of end-point continuum-solvation methods for the calculation of protein-ligand binding free energies.
    Genheden S, Ryde U.
    Proteins; 2012 May 07; 80(5):1326-42. PubMed ID: 22274991
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