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Predicting binding modes, binding affinities and ‘hot spots’ for protein-ligand complexes using a knowledge-based scoring function

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Virtual Screening: An Alternative or Complement to High Throughput Screening?

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References

  1. Muller, K., Perspect. Drug Discov. Design, 3 (1995) v.

    Google Scholar 

  2. Walters, W.P., Stahl, M.T. and Murcko, M.A., Drug Discov. Today, 3 (1998) 160.

    Article  CAS  Google Scholar 

  3. Van Drie, J.H. and Lajiness, M.S., Drug Discov. Today, 3 (1998) 274.

    Google Scholar 

  4. Kubinyi, H., Curr. Opin. Drug Discov. Develop., 1 (1998) 4.

    CAS  Google Scholar 

  5. Lengauer, T. and Rarey, M., Curr. Opin. Struct. Biol., 6 (1996) 402.

    Article  PubMed  CAS  Google Scholar 

  6. Kuntz, I.D., Meng, E.C. and Shoichet, B.K., Acc. Chem. Res., 27 (1994) 117.

    Article  CAS  Google Scholar 

  7. Rarey, M., Kramer, B., Lengauer, T. and Klebe, G., J. Mol. Biol., 261 (1996) 470.

    Article  PubMed  CAS  Google Scholar 

  8. Kuntz, I.D., Blaney, J.M., Oatley, S.J., Langridge, R. and Ferrin, T.E., J. Mol. Biol., 161 (1982) 269.

    Article  PubMed  CAS  Google Scholar 

  9. Jones, G., Willett, P., Glen, R.C., Leach, A.R. and Taylor, R., J. Mol. Biol., 267 (1997) 727.

    Article  PubMed  CAS  Google Scholar 

  10. Dixon, J.S., Proteins, Suppl. 1, (1997) 198.

    Google Scholar 

  11. Beveridge, D.L. and DiCapua, EM., Annu. Rev. Biophys. Biophys. Chem., 18 (1989) 431.

    Article  PubMed  CAS  Google Scholar 

  12. Kollman, P., Chem. Rev., 93 (1993) 2395.

    Article  CAS  Google Scholar 

  13. Kollman, P.A., Acc. Chem. Res., 29 (1996) 461.

    Article  CAS  Google Scholar 

  14. Dill, K.A., J. Biol. Chem., 272 (1997) 701.

    PubMed  CAS  Google Scholar 

  15. Böhm, H.J., J. Comput.-Aided Mol. Design, 8 (1994) 243.

    Google Scholar 

  16. Böhm, H.J., J. Comput.-Aided Mol. Design, 12 (1998) 309.

    Google Scholar 

  17. Jain, A.N., J. Comput.-Aided Mol. Design, 10 (1996) 427.

    Article  CAS  Google Scholar 

  18. Murray, C.W., Auton, T.R. and Eldridge, M.D., J. Comput.-Aided Mol. Design, 12 (1998) 503.

    Article  CAS  Google Scholar 

  19. Rose, P. W., Scoring methods in ligand design, Proceedings of 2nd UCSF Course in Computer-Aided Molecular Design, San Francisco, CA, 1997.

    Google Scholar 

  20. Head, R.D., Smythe, M.L., Oprea, T.I., Waller, C.L., Green, S.M. and Marshall, G.R., J. Am. Chem. Soc., 118 (1996) 3959.

    Article  CAS  Google Scholar 

  21. Stahl, M. and Böhm, H.-J., J. Mol. Graph. Model, 16 (1998) 121.

    PubMed  CAS  Google Scholar 

  22. Vajda, S., Sippl, M. and Novotny, J., Curr. Opin. Struct. Biol., 7 (1997) 222.

    Article  PubMed  CAS  Google Scholar 

  23. Jernigan, R.L. and Bahar, I., Curr. Opin. Struct. Biol., 6 (1996) 195.

    Article  PubMed  CAS  Google Scholar 

  24. Torda, A.E., Curr. Opin. Struct. Biol., 7 (1997) 200.

    Article  PubMed  CAS  Google Scholar 

  25. Mitchell, J.B.O., Laskowski, R.A., Alex, A., Forster, M.J. and Thornton, J.M., J. Comput. Chem., 20 (1999) 1177.

    CAS  Google Scholar 

  26. Wallqvist, A. and Covell, D.G., Proteins, 25 (1996) 403.

    PubMed  CAS  Google Scholar 

  27. Wallqvist, A., Jernigan, R.L. and Covell, D.G., Protein Sci., 4 (1995) 1881.

    PubMed  CAS  Google Scholar 

  28. Verkhivker, K., Appelt, K., Freer, S.T. and Villafranca, J.E., Protein Eng., 8 (1995) 677.

    Article  PubMed  CAS  Google Scholar 

  29. Sharp, K.A., Nicholls, A., Friedman, R. and Honig, B., Biochemistry, 30 (1991) 9686.

    Article  PubMed  CAS  Google Scholar 

  30. Pickett, S.D. and Sternberg, M.J., J. Mol. Biol., 231 (1993) 825.

    Article  PubMed  CAS  Google Scholar 

  31. DeWitte, R.S. and Shaknovich, E.I., J. Am. Chem. Soc., 118 (1996) 11733.

    Article  CAS  Google Scholar 

  32. Bernstein, F.C., Koetzle, T.F., Williams, G.J., Meyer Jr., E.E., Brice, M.D., Rodgers, J.R., Kennard, O., Shimanouchi, T. and Tasumi, M., J. Mol. Biol., 112 (1977) 535.

    PubMed  CAS  Google Scholar 

  33. Muegge, I. and Martin, Y.C., J. Med. Chem., 42 (1999) 791.

    PubMed  CAS  Google Scholar 

  34. Muegge, I., Martin, Y.C., Hajduk, P.J. and Fesik, S.W., J. Med. Chem., 42 (1999) 2498.

    PubMed  CAS  Google Scholar 

  35. Mitchell, J.B.O., Laskowski, R.A., Alex, A. and Thornton, J.M., J. Comput. Chem., 20 (1999) 1165.

    CAS  Google Scholar 

  36. Gohlke, H., Hendlich, K. and Klebe, G., J. Mol. Biol., 295 (2000) 337.

    Article  PubMed  CAS  Google Scholar 

  37. Hendlich, M., Acta Crystallogr., D 54 (1998) 1178.

    Article  CAS  Google Scholar 

  38. Verdonk, M.L., Cole, J.C. and Taylor, R., J. Mol. Biol., 289 (1999) 1093.

    Article  PubMed  CAS  Google Scholar 

  39. Bohm, H.-J. and Klebe, G., Angew. Chem. Int. Ed. Engl., 35 (1996) 2566.

    Google Scholar 

  40. Sippl, M.J., Curr. Opin. Struct. Biol., 5 (1995) 229.

    Article  PubMed  CAS  Google Scholar 

  41. Sippl, M.J., J. Mol. Biol., 213 (1990) 859.

    PubMed  CAS  Google Scholar 

  42. Sippl, M.J., J. Comput.-Aided Mol. Design, 7 (1993) 473.

    CAS  Google Scholar 

  43. Godzik, A., Kolinski, A. and Skolnick, J., Protein Sci., 4 (1995) 2107.

    Article  PubMed  CAS  Google Scholar 

  44. Miyazawa, S. and Jernigan, R.L., Proteins, 34 (1999) 49.

    Article  PubMed  CAS  Google Scholar 

  45. Koehl, P. and Delarue, M., Proteins, 20 (1994) 264.

    Article  PubMed  CAS  Google Scholar 

  46. Testa, B., Carrupt, P.A., Gaillard, P., Billois, F. and Weber, P., Pharm. Res., 13 (1996) 335.

    Article  PubMed  CAS  Google Scholar 

  47. SYBYL, Tripos Inc., St. Louis, MO.

    Google Scholar 

  48. Davis, A.M. and Teague, S.J., Angew. Chem. Int. Ed. Engl., 38 (1999) 736.

    Article  CAS  Google Scholar 

  49. Burley, S.K. and Petsko, G.A., Science, 229 (1985) 23.

    PubMed  CAS  Google Scholar 

  50. Eldridge, M.D., Murray, C.W., Auton, T.R., Paolini, G.V. and Mee, R.P., J. Comput.-Aided Mol. Design, 11 (1997) 425.

    Article  CAS  Google Scholar 

  51. Hosur, M.V., Bhat, T.N., Kempf, D.J., Baldwin, E.T., Liu, B., Gulnik, S., Wideburg, N.E., Norbeck, D.W., Appelt, K. and Erickson, J.W., J. Am. Chem. Soc., 116 (1994) 847.

    Article  CAS  Google Scholar 

  52. Kramer, B., Rarey, M. and Lengauer, T., Proteins, 37 (1999) 145.

    Article  Google Scholar 

  53. Quiocho, EA., Wilson, D.K. and Vyas, N.K., Nature, 340 (1989) 404.

    Article  PubMed  CAS  Google Scholar 

  54. Obst, U., De novo-Designund Synthese neuartiger, nichtpeptidischer Thrombin-Inhibitoren, Ph.D. Thesis, ETH Zurich, Zurich, 1997. 252.

    Google Scholar 

  55. Obst, U., Banner, D.W., Weber, L. and Diederich, F., Chem. Biol., 4 (1997) 287.

    Article  PubMed  CAS  Google Scholar 

  56. De Priest, S.A., Mayer, D., Naylor, C.B. and Marshall, G.R., J. Am. Chem. Soc., 115 (1993) 5372.

    Google Scholar 

  57. Bruno, I.J., Cole, J.C., Lommerse, J.P., Rowland, R.S., Taylor, R. and Verdonk, M.L., J. Comput.-Aided Mol. Design, 11 (1997) 525.

    Article  CAS  Google Scholar 

  58. Bartlett, P.A. and Marlowe, C.K., Science, 235 (1987) 569.

    PubMed  CAS  Google Scholar 

  59. Grobelny, D., Goli, U.B. and Galardy, R.E., Biochemistry, 28 (1989) 4948.

    Article  PubMed  CAS  Google Scholar 

  60. Weiner, S.J., Kollman, P.A., Case, D.A., Singh, U.C., Ghio, C., Alagona, G., Profeta, S. and Weiner, P., J. Am. Chem. Soc., 106 (1984) 765.

    CAS  Google Scholar 

  61. Allen, F.H., Davies, J.E., Galloy, J.J., Johnson, O., Kennard, O., Macrae, C.F., Mitchell, E.M., Mitchell, G.F., Smith, J.M. and Watson, D.G., J. Chem. Inf. Comput. Sci., 31 (1991) 187.

    Article  CAS  Google Scholar 

  62. Hofmann, D.W.M. and Lengauer, T., J. Mol. Model, 4 (1998) 132.

    Article  CAS  Google Scholar 

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Author information

Authors and Affiliations

  1. Department of Pharmaceutical Chemistry, Philipps-University of Marburg, Marbacher Weg 6, D-35032, Marburg, Germany

    Holger Gohlke, Manfred Hendlich & Gerhard Klebe

Authors
  1. Holger Gohlke
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  2. Manfred Hendlich
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  3. Gerhard Klebe
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Editor information

Editors and Affiliations

  1. Institute of Pharmaceutical Chemistry, Philipps University of Marburg, Marbacher Weg 6, D-35032, Marburg, Germany

    Gerhard Klebe

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© 2000 Kluwer Academic Publishers

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Gohlke, H., Hendlich, M., Klebe, G. (2000). Predicting binding modes, binding affinities and ‘hot spots’ for protein-ligand complexes using a knowledge-based scoring function. In: Klebe, G. (eds) Virtual Screening: An Alternative or Complement to High Throughput Screening?., vol 20. Springer, Dordrecht. https://doi.org/10.1007/0-306-46883-2_8

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  • DOI: https://doi.org/10.1007/0-306-46883-2_8

  • Publisher Name: Springer, Dordrecht

  • Print ISBN: 978-0-7923-6633-1

  • Online ISBN: 978-0-306-46883-4

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