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Knowledge-based prediction of protein structures and the design of novel molecules

Abstract

Prediction of the tertiary structures of proteins may be carried out using a knowledge-based approach. This depends on identification of analogies in secondary structures, motifs, domains or ligand interactions between a protein to be modelled and those of known three-dimensional structures. Such techniques are of value in prediction of receptor structures to aid the design of drugs, herbicides or pesticides, antigens in vaccine design, and novel molecules in protein engineering.

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References

  1. Blundell, T. L. et al. Phil. Trans. R. Soc. A 317, 333–344 (1986).

    Article  ADS  CAS  Google Scholar 

  2. Porter, R. & Whelan, J. (eds) Synthetic Peptides as Antigens, CIBA Foundation Symposium 119 (Wiley, Avon, 1986).

  3. Haddon, R. C. & Lamola, A. A. Proc. natn. Acad. Sci. U.S.A. 82, 1874–1878 (1985).

    Article  ADS  CAS  Google Scholar 

  4. Wagner, G. & Wuthrich, K. J. molec. Biol. 155, 347–366 (1982).

    Article  CAS  Google Scholar 

  5. Winter, G. & Fersht, A. R. Trends Biotechnol. 2, 115–119 (1984).

    Article  CAS  Google Scholar 

  6. Richards, W. G. (ed.) J. molec. Graphics 4, 1–73 (1986).

  7. Brooks, B. & Karplus, M. Proc. natn. Acad. Sci. U.S.A. 80, 6571–6575 (1983).

    Article  ADS  CAS  Google Scholar 

  8. Kneale, G. G. & Bishop, M. J. Cabios Rev. 1, 11–17 (1985).

    CAS  Google Scholar 

  9. Needleman, S. B. & Wunsch, C. D. J. molec. Biol. 48, 443–453 (1970).

    Article  CAS  Google Scholar 

  10. Sellers, P. J. appl. Math. 26, 787–793 (1974).

    Google Scholar 

  11. Waterman, M. S., Smith, T. F. & Beyer, W. A. Adv. Math. 20, 367–387 (1976).

    Article  Google Scholar 

  12. Fitch, W. M. & Smith, T. F. Proc. natn. Acad. Sci. U.S.A. 80, 1382–2386 (1983).

    Article  ADS  CAS  Google Scholar 

  13. Barton, G. & Sternberg, M. J. E. Protein Engng (in the press).

  14. Lesk, A., Levitt, M. & Chothia, C. Protein Engng 1, 77–78 (1987).

    Article  Google Scholar 

  15. Gooad, W. B. & Kanehisa, M. I. Nucleic Acids Res. 10, 247–263 (1982).

    Article  Google Scholar 

  16. Sellers, P. Proc. natn. Acad. Sci. U.S.A. 76, 3041–3044 (1979).

    Article  ADS  CAS  Google Scholar 

  17. Boswell, D. R. & McLachlan, A. D. Nucleic Acids Res. 12, 457–464 (1984).

    Article  CAS  Google Scholar 

  18. Taylor, W. R. J. molec. Biol. 188, 233–258 (1986).

    Article  CAS  Google Scholar 

  19. Bajaj, M. & Blundell, T. L. A. Rev. Biophys. Bioengng 13, 453–492 (1984).

    Article  CAS  Google Scholar 

  20. Greer, J. J. molec. Biol. 153, 1027–1042 (1981).

    Article  CAS  Google Scholar 

  21. Richardson, J. S., Getzoff, E. D. & Richardson, D. C. Proc. natn. Acad. Sci. U.S.A. 75, 2574–2578 (1978).

    Article  ADS  CAS  Google Scholar 

  22. Cutfield, J. F. et al. in Structural Studies on Molecules of Biological Interest (ed. Dodson, G. C.) 501–508 (Clarendon Press, Oxford, 1981).

    Google Scholar 

  23. Lesk, A. M. & Chothia, C. J. molec. Biol. 136, 225–270 (1980).

    Article  CAS  Google Scholar 

  24. Lesk, A. M. & Chothia, C. J. molec. Biol. 160, 325–342 (1982).

    Article  CAS  Google Scholar 

  25. Chothia, C. & Lesk, A. M. J. molec. Biol. 160, 309–323 (1982).

    Article  CAS  Google Scholar 

  26. Chothia, C. & Lesk, A. M. EMBO J. 5, 823–826 (1986).

    Article  CAS  Google Scholar 

  27. Hubbard, T. & Blundell, T. L. Prot. Engng (submitted).

  28. Browne, W. J. et al. J. molec. Biol. 120, 97–120 (1969).

    Google Scholar 

  29. Jones, A. T. J. appl. Cryst. 11, 268–272 (1978).

    Article  CAS  Google Scholar 

  30. Palmer, K. A., Scheraga, H. A., Riordan, J. F. & Vallee, R. Z. Proc. natn. Acad. Sci. U.S.A. 83, 1965–1969 (1986).

    Article  ADS  CAS  Google Scholar 

  31. Isaacs, N. et al. Nature 271, 278–281 (1978).

    Article  ADS  CAS  Google Scholar 

  32. Bedarkar, S. et al. Nature 270, 449–451 (1977).

    Article  ADS  CAS  Google Scholar 

  33. Blundell, T. L., Bedarkar, S. & Humbel, R. E. Proc. natn. Acad. Sci. U.S.A. 75, 180–184 (1978).

    Article  ADS  CAS  Google Scholar 

  34. Travers, P. et al. Nature 310, 235–278 (1984).

    Article  ADS  CAS  Google Scholar 

  35. Blundell, T. L., Sibanda, B. L. & Pearl, L. H. Nature 304, 273–275 (1983).

    Article  ADS  CAS  Google Scholar 

  36. Sibanda, B. L. et al. FEBS Lett. 174, 103–111 (1984).

    Article  Google Scholar 

  37. Carlson, W., Karplus, M. & Haber, E. Hypertension 7, 13–26 (1985).

    Article  CAS  Google Scholar 

  38. Akahone, P. et al. Hypertension 7, 3–12 (1985).

    Article  Google Scholar 

  39. Chothia, C. et al. Science 233, 755–758 (1986).

    Article  ADS  CAS  Google Scholar 

  40. La Paz, P., Sutton, B. R., Darsley, M. J. & Rees, A. R. EMBO J. 5, 415–425 (1986).

    Article  Google Scholar 

  41. Ripka, W. C. Nature 321, 93–94 (1986).

    Article  ADS  Google Scholar 

  42. O'Neil, K. & De Grado, W. F. Proc. natn. Acad. Sci. U.S.A. 82, 4954–4958 (1985).

    Article  ADS  CAS  Google Scholar 

  43. Sutcliffe, M. & Haneef, I. Inf. Q. Prot. Cryst. 18, 11–18 (1986).

    Google Scholar 

  44. Read, R. J., Fujinaga, M., Sielecki, A. R. & James, M. N. G. Biochemistry 22, 4420–4433 (1983).

    Article  CAS  Google Scholar 

  45. Read, R. J., Brayer, G. D., Jarasek, L. & James, M. N. G. Biochemistry 23, 6570–6575 (1984).

    Article  CAS  Google Scholar 

  46. Sibanda, B. L. & Thornton, J. M. Nature 316, 170–174 (1985).

    Article  ADS  CAS  Google Scholar 

  47. Edwards, M., Sternberg, M. J. E. & Thornton, J. M. Prot. Engng (in the press).

  48. Moult, J. & James, M. N. Proteins 2, 146–163 (1986).

    Article  Google Scholar 

  49. Milner-White, J. & Poet, R. Biochem. J. 240, 289–292 (1986).

    Article  CAS  Google Scholar 

  50. Sibanda, B. L. thesis, Univ. London (1986).

  51. Jones, T. A. & Sirup, T. EMBO J. 5, 819–822 (1986).

    Article  CAS  Google Scholar 

  52. Crippen, G. M. in Chemometric Research Studies Series Vol. 1 (ed. Bandan, D.) 1–58 (Wiley, New York, 1981).

    Google Scholar 

  53. Weiner, S. J. et al. J. Am. chem. Soc. 106, 765–784 (1984).

    Article  CAS  Google Scholar 

  54. Brooks, B. R. J. Computation Chem. 4, 187–217 (1983).

    Article  CAS  Google Scholar 

  55. Shih, H. L., Brady, J. & Karplus, M. Proc. natn. Acad. Sci. U.S.A. 82, 1697–1700 (1985).

    Article  ADS  CAS  Google Scholar 

  56. Hagler, A. T. & Moult, J. Nature 272, 222–227 (1979).

    Article  ADS  Google Scholar 

  57. Wodak, S. J., Alard, P., Delhouse, P. & Renneboog-Squilbin, C., J. molec. Biol. 181, 317–322 (1984).

    Article  Google Scholar 

  58. Robson, B. & Platt, E. J. molec. Biol. 188, 259–281.

  59. Summers, L. D. et al. Expl Eye Res. 43, 77–92 (1986).

    Article  CAS  Google Scholar 

  60. Driessen, H. P. C. & White, H. in Molecular Replacement (ed. Machin, P. A.) 27–32 (Daresbury Laboratory, Daresbury, 1985).

    Google Scholar 

  61. Amit, A. G. et al. Science 233, 747–753 (1986).

    Article  ADS  CAS  Google Scholar 

  62. Novotny, J., Bruccoleri, R. & Karplus, M. J. molec. Biol. 177, 787–818 (1984).

    Article  CAS  Google Scholar 

  63. Banner et al. Nature 255, 609–614 (1975).

    Article  ADS  CAS  Google Scholar 

  64. Abad-Zapatero, C. et al. Nature 286, 33–39 (1980).

    Article  ADS  CAS  Google Scholar 

  65. Wistow, G., Summers, L. J. & Blundell, T. L. Nature 315, 771–773 (1985).

    Article  ADS  CAS  Google Scholar 

  66. Wieranga, R. K. & Hol, W. G. Nature 302, 842–844 (1983).

    Article  ADS  Google Scholar 

  67. Sternberg, M. J. E. & Taylor, W. R. FEBS Lett. 175, 387–392 (1984).

    Article  CAS  Google Scholar 

  68. Neuberger, M. S., Williams, G. T. & Fox, R. O. Nature 312, 604–608 (1984).

    Article  ADS  CAS  Google Scholar 

  69. Hemmings, A., Foundling, S., Sibanda, B. L., Wood, S. P. & Blundell, T. L. Trans. Biochem. Soc. 13, 1036–1041 (1985).

    Article  CAS  Google Scholar 

  70. Thomas, K. A., Smith, G. M., Thomas, T. J. & Feldmann, R. J., Proc. natn. Acad. Sci. 79, 4843–4847 (1982).

    Article  ADS  CAS  Google Scholar 

  71. Reid, K. S. C., Lindley, P. F. & Thornton, J. M. FEBS Lett. 190, 209–213 (1985).

    Article  CAS  Google Scholar 

  72. Singh, J. & Thornton, J. M. FEBS Lett. 191, 1–6 (1985).

    Article  CAS  Google Scholar 

  73. Nussenzweig, V. & Nussenzweig, R. in Ciba Foundation Symposium 119 (eds Porter, R. & Whelan, J.) 150–163 (Wiley, Avon, 1986).

    Google Scholar 

  74. Geysen, H. M., Rodda, S. J. & Mason, T. J. in Ciba Foundation Symposium 119 (eds Porter, R. & Whelan, J.) 130–149 (Wiley, Avon, 1986).

    Google Scholar 

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Blundell, T., Sibanda, B., Sternberg, M. et al. Knowledge-based prediction of protein structures and the design of novel molecules. Nature 326, 347–352 (1987). https://doi.org/10.1038/326347a0

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