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Journal Abstract Search

220 related items for PubMed ID: 21466174

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  • 2. A reliable docking/scoring scheme based on the semiempirical quantum mechanical PM6-DH2 method accurately covering dispersion and H-bonding: HIV-1 protease with 22 ligands.
    Fanfrlík J, Bronowska AK, Rezác J, Prenosil O, Konvalinka J, Hobza P.
    J Phys Chem B; 2010 Oct 07; 114(39):12666-78. PubMed ID: 20839830
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  • 7. Empirical free energy calculations of human immunodeficiency virus type 1 protease crystallographic complexes. II. Knowledge-based ligand-protein interaction potentials applied to thermodynamic analysis of hydrophobic mutations.
    Verkhivker GM.
    Pac Symp Biocomput; 1996 Oct 07; ():638-52. PubMed ID: 9390264
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  • 8. The treatment of solvation by a generalized Born model and a self-consistent charge-density functional theory-based tight-binding method.
    Xie L, Liu H.
    J Comput Chem; 2002 Nov 30; 23(15):1404-15. PubMed ID: 12370943
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  • 9. Fragment-Based flexible ligand docking by evolutionary optimization.
    Budin N, Majeux N, Caflisch A.
    Biol Chem; 2001 Sep 30; 382(9):1365-72. PubMed ID: 11688719
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  • 10. Structural parameterization of the binding enthalpy of small ligands.
    Luque I, Freire E.
    Proteins; 2002 Nov 01; 49(2):181-90. PubMed ID: 12210999
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  • 11. Structure, dynamics and solvation of HIV-1 protease/saquinavir complex in aqueous solution and their contributions to drug resistance: molecular dynamic simulations.
    Wittayanarakul K, Aruksakunwong O, Sompornpisut P, Sanghiran-Lee V, Parasuk V, Pinitglang S, Hannongbua S.
    J Chem Inf Model; 2005 Nov 01; 45(2):300-8. PubMed ID: 15807491
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  • 12. Assessing scoring functions for protein-ligand interactions.
    Ferrara P, Gohlke H, Price DJ, Klebe G, Brooks CL.
    J Med Chem; 2004 Jun 03; 47(12):3032-47. PubMed ID: 15163185
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  • 13. Large-scale validation of a quantum mechanics based scoring function: predicting the binding affinity and the binding mode of a diverse set of protein-ligand complexes.
    Raha K, Merz KM.
    J Med Chem; 2005 Jul 14; 48(14):4558-75. PubMed ID: 15999994
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  • 15. Explicit solvent dynamics and energetics of HIV-1 protease flap opening and closing.
    Sadiq SK, De Fabritiis G.
    Proteins; 2010 Nov 01; 78(14):2873-85. PubMed ID: 20715057
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  • 16. Absolute and relative binding free energy calculations of the interaction of biotin and its analogs with streptavidin using molecular dynamics/free energy perturbation approaches.
    Miyamoto S, Kollman PA.
    Proteins; 1993 Jul 01; 16(3):226-45. PubMed ID: 8346190
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  • 18. A semiempirical free energy force field with charge-based desolvation.
    Huey R, Morris GM, Olson AJ, Goodsell DS.
    J Comput Chem; 2007 Apr 30; 28(6):1145-52. PubMed ID: 17274016
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  • 19. Estimating protein-ligand binding free energy: atomic solvation parameters for partition coefficient and solvation free energy calculation.
    Pei J, Wang Q, Zhou J, Lai L.
    Proteins; 2004 Dec 01; 57(4):651-64. PubMed ID: 15390269
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