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185 related items for PubMed ID: 16107145

  • 1. Improving binding mode predictions by docking into protein-specifically adapted potential fields.
    Radestock S, Böhm M, Gohlke H.
    J Med Chem; 2005 Aug 25; 48(17):5466-79. PubMed ID: 16107145
    [Abstract] [Full Text] [Related]

  • 2. A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance.
    Perola E, Walters WP, Charifson PS.
    Proteins; 2004 Aug 01; 56(2):235-49. PubMed ID: 15211508
    [Abstract] [Full Text] [Related]

  • 3. DrugScore(CSD)-knowledge-based scoring function derived from small molecule crystal data with superior recognition rate of near-native ligand poses and better affinity prediction.
    Velec HF, Gohlke H, Klebe G.
    J Med Chem; 2005 Oct 06; 48(20):6296-303. PubMed ID: 16190756
    [Abstract] [Full Text] [Related]

  • 4. Consensus adaptation of fields for molecular comparison (AFMoC) models incorporate ligand and receptor conformational variability into tailor-made scoring functions.
    Breu B, Silber K, Gohlke H.
    J Chem Inf Model; 2007 Oct 06; 47(6):2383-400. PubMed ID: 17958410
    [Abstract] [Full Text] [Related]

  • 5. 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
    [Abstract] [Full Text] [Related]

  • 6. AFMoC enhances predictivity of 3D QSAR: a case study with DOXP-reductoisomerase.
    Silber K, Heidler P, Kurz T, Klebe G.
    J Med Chem; 2005 May 19; 48(10):3547-63. PubMed ID: 15887963
    [Abstract] [Full Text] [Related]

  • 7. A method for induced-fit docking, scoring, and ranking of flexible ligands. Application to peptidic and pseudopeptidic beta-secretase (BACE 1) inhibitors.
    Moitessier N, Therrien E, Hanessian S.
    J Med Chem; 2006 Oct 05; 49(20):5885-94. PubMed ID: 17004704
    [Abstract] [Full Text] [Related]

  • 8. A general and fast scoring function for protein-ligand interactions: a simplified potential approach.
    Muegge I, Martin YC.
    J Med Chem; 1999 Mar 11; 42(5):791-804. PubMed ID: 10072678
    [Abstract] [Full Text] [Related]

  • 9. 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
    [Abstract] [Full Text] [Related]

  • 10. Computational design of novel fullerene analogues as potential HIV-1 PR inhibitors: Analysis of the binding interactions between fullerene inhibitors and HIV-1 PR residues using 3D QSAR, molecular docking and molecular dynamics simulations.
    Durdagi S, Mavromoustakos T, Chronakis N, Papadopoulos MG.
    Bioorg Med Chem; 2008 Dec 01; 16(23):9957-74. PubMed ID: 18996019
    [Abstract] [Full Text] [Related]

  • 11. Refining the multiple protein structure pharmacophore method: consistency across three independent HIV-1 protease models.
    Meagher KL, Lerner MG, Carlson HA.
    J Med Chem; 2006 Jun 15; 49(12):3478-84. PubMed ID: 16759090
    [Abstract] [Full Text] [Related]

  • 12. Predicting multiple ligand binding modes using self-consistent pharmacophore hypotheses.
    Wallach I, Lilien R.
    J Chem Inf Model; 2009 Sep 15; 49(9):2116-28. PubMed ID: 19711952
    [Abstract] [Full Text] [Related]

  • 13. Ensemble docking of multiple protein structures: considering protein structural variations in molecular docking.
    Huang SY, Zou X.
    Proteins; 2007 Feb 01; 66(2):399-421. PubMed ID: 17096427
    [Abstract] [Full Text] [Related]

  • 14. DrugScore meets CoMFA: adaptation of fields for molecular comparison (AFMoC) or how to tailor knowledge-based pair-potentials to a particular protein.
    Gohlke H, Klebe G.
    J Med Chem; 2002 Sep 12; 45(19):4153-70. PubMed ID: 12213058
    [Abstract] [Full Text] [Related]

  • 15. Towards a MIP-based alignment and docking in computer-aided drug design.
    Barbany M, Gutiérrez-de-Terán H, Sanz F, Villà-Freixa J.
    Proteins; 2004 Aug 15; 56(3):585-94. PubMed ID: 15229890
    [Abstract] [Full Text] [Related]

  • 16. Incorporating protein flexibility in structure-based drug discovery: using HIV-1 protease as a test case.
    Meagher KL, Carlson HA.
    J Am Chem Soc; 2004 Oct 20; 126(41):13276-81. PubMed ID: 15479081
    [Abstract] [Full Text] [Related]

  • 17. Coarse-grained molecular dynamics of ligands binding into protein: The case of HIV-1 protease inhibitors.
    Li D, Liu MS, Ji B, Hwang K, Huang Y.
    J Chem Phys; 2009 Jun 07; 130(21):215102. PubMed ID: 19508101
    [Abstract] [Full Text] [Related]

  • 18. Prediction of the binding energy for small molecules, peptides and proteins.
    Schapira M, Totrov M, Abagyan R.
    J Mol Recognit; 1999 Jun 07; 12(3):177-90. PubMed ID: 10398408
    [Abstract] [Full Text] [Related]

  • 19. Structure-based ligand design by dynamically assembling molecular building blocks at binding site.
    Liu H, Duan Z, Luo Q, Shi Y.
    Proteins; 1999 Sep 01; 36(4):462-70. PubMed ID: 10450088
    [Abstract] [Full Text] [Related]

  • 20. A critical assessment of docking programs and scoring functions.
    Warren GL, Andrews CW, Capelli AM, Clarke B, LaLonde J, Lambert MH, Lindvall M, Nevins N, Semus SF, Senger S, Tedesco G, Wall ID, Woolven JM, Peishoff CE, Head MS.
    J Med Chem; 2006 Oct 05; 49(20):5912-31. PubMed ID: 17004707
    [Abstract] [Full Text] [Related]

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