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Journal Abstract Search

141 related items for PubMed ID: 19928836

  • 1. Docking ligands into flexible and solvated macromolecules. 5. Force-field-based prediction of binding affinities of ligands to proteins.
    Englebienne P, Moitessier N.
    J Chem Inf Model; 2009 Nov; 49(11):2564-71. PubMed ID: 19928836
    [Abstract] [Full Text] [Related]

  • 2. Docking ligands into flexible and solvated macromolecules. 4. Are popular scoring functions accurate for this class of proteins?
    Englebienne P, Moitessier N.
    J Chem Inf Model; 2009 Jun; 49(6):1568-80. PubMed ID: 19445499
    [Abstract] [Full Text] [Related]

  • 3. Investigation of MM-PBSA rescoring of docking poses.
    Thompson DC, Humblet C, Joseph-McCarthy D.
    J Chem Inf Model; 2008 May; 48(5):1081-91. PubMed ID: 18465849
    [Abstract] [Full Text] [Related]

  • 4. 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
    [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. Lead finder: an approach to improve accuracy of protein-ligand docking, binding energy estimation, and virtual screening.
    Stroganov OV, Novikov FN, Stroylov VS, Kulkov V, Chilov GG.
    J Chem Inf Model; 2008 Dec 03; 48(12):2371-85. PubMed ID: 19007114
    [Abstract] [Full Text] [Related]

  • 7. Optimizing the signal-to-noise ratio of scoring functions for protein--ligand docking.
    Seifert MH.
    J Chem Inf Model; 2008 Mar 03; 48(3):602-12. PubMed ID: 18293951
    [Abstract] [Full Text] [Related]

  • 8. 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]

  • 9. New scoring functions for virtual screening from molecular dynamics simulations with a quantum-refined force-field (QRFF-MD). Application to cyclin-dependent kinase 2.
    Ferrara P, Curioni A, Vangrevelinghe E, Meyer T, Mordasini T, Andreoni W, Acklin P, Jacoby E.
    J Chem Inf Model; 2006 Aug 01; 46(1):254-63. PubMed ID: 16426061
    [Abstract] [Full Text] [Related]

  • 10. Protein flexibility in ligand docking and virtual screening to protein kinases.
    Cavasotto CN, Abagyan RA.
    J Mol Biol; 2004 Mar 12; 337(1):209-25. PubMed ID: 15001363
    [Abstract] [Full Text] [Related]

  • 11. Development and evaluation of a generic evolutionary method for protein-ligand docking.
    Yang JM.
    J Comput Chem; 2004 Apr 30; 25(6):843-57. PubMed ID: 15011256
    [Abstract] [Full Text] [Related]

  • 12. Comparative evaluation of 11 scoring functions for molecular docking.
    Wang R, Lu Y, Wang S.
    J Med Chem; 2003 Jun 05; 46(12):2287-303. PubMed ID: 12773034
    [Abstract] [Full Text] [Related]

  • 13. An extensive test of 14 scoring functions using the PDBbind refined set of 800 protein-ligand complexes.
    Wang R, Lu Y, Fang X, Wang S.
    J Chem Inf Comput Sci; 2004 Jun 05; 44(6):2114-25. PubMed ID: 15554682
    [Abstract] [Full Text] [Related]

  • 14. The consequences of scoring docked ligand conformations using free energy correlations.
    Spyrakis F, Amadasi A, Fornabaio M, Abraham DJ, Mozzarelli A, Kellogg GE, Cozzini P.
    Eur J Med Chem; 2007 Jul 05; 42(7):921-33. PubMed ID: 17346861
    [Abstract] [Full Text] [Related]

  • 15. Scoring ligand similarity in structure-based virtual screening.
    Zavodszky MI, Rohatgi A, Van Voorst JR, Yan H, Kuhn LA.
    J Mol Recognit; 2009 Jul 05; 22(4):280-92. PubMed ID: 19235177
    [Abstract] [Full Text] [Related]

  • 16. Testing assumptions and hypotheses for rescoring success in protein-ligand docking.
    O'Boyle NM, Liebeschuetz JW, Cole JC.
    J Chem Inf Model; 2009 Aug 05; 49(8):1871-8. PubMed ID: 19645429
    [Abstract] [Full Text] [Related]

  • 17. Binding energy landscape analysis helps to discriminate true hits from high-scoring decoys in virtual screening.
    Wei D, Zheng H, Su N, Deng M, Lai L.
    J Chem Inf Model; 2010 Oct 25; 50(10):1855-64. PubMed ID: 20968314
    [Abstract] [Full Text] [Related]

  • 18. 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]

  • 19. 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]

  • 20. Impact of scoring functions on enrichment in docking-based virtual screening: an application study on renin inhibitors.
    Krovat EM, Langer T.
    J Chem Inf Comput Sci; 2004 Mar 11; 44(3):1123-9. PubMed ID: 15154781
    [Abstract] [Full Text] [Related]

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