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Ligand-receptor docking with the Mining Minima optimizer

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Abstract

The optimizer developed for the Mining Minima algorithm, which uses ideas from Genetic Algorithms, the Global Underestimator Method, and Poling, has been adapted for use in ligand-receptor docking. The present study describes the resulting methodology and evaluates its accuracy and speed for 27 test systems. The performance of the new docking algorithm appears to be competitive with that of previously published methods. The energy model, an empirical force field with a distance-dependent dielectric treatment of solvation, is adequate for a number of test cases, although incorrect low-energy conformations begin to compete with the correct conformation for larger sampling volumes and for highly solvent-exposed binding sites that impose little steric constraint on the ligand.

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References

  1. Head, M.S., Given, J.A. and Gilson, M.K., J. Phys. Chem., 101 (1997) 1609.

    Google Scholar 

  2. Phillips, A.T., Rosen, J.B. and Walke, V.H., Dimacs Series in Discrete Math. Theoret. Comput. Sci., 23 (1995) 181.

    Google Scholar 

  3. Holland, J.H. Adaptation in Natural and Artificial Systems. MIT Press, Cambridge, MA, 1975.

    Google Scholar 

  4. DeJong, An analysis of the behavior of a class of genetic adaptive systems, Phd Thesis, Michigan, 1975.

  5. Goldberg, D.E. Genetic Algorithms in Search, Optimisation and Machine Learning. Addison Wesley, Reading, MA, 1989.

    Google Scholar 

  6. Smellie, A., Teig, S.L. and Towbin, P., J. Comput. Chem., 16 (1995) 171.

    Google Scholar 

  7. Glover, F. and Laguna, M. Tabu Search, Kluwer Academic Publishers, Dordrecht, 1997.

    Google Scholar 

  8. Westhead, D.R., Clark, D.E. and Murray, C.W., J. Comput. Aid. Mol. Des., 11 (1997) 209.

    Google Scholar 

  9. Baxter, C.A., Murray, C.W., Clark, D.E., Westhead, D.R. and Eldridge, M.D., Proteins, 33 (1998) 367.

    PubMed  Google Scholar 

  10. Morris, G.M., Goodsell, D.S., Halliday, R.S., Huey, R., Hart, W.E., Belew, R.K. and Olson, A.J., J. Comp. Chem., 19 (1998) 1639.

    Google Scholar 

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

    PubMed  Google Scholar 

  12. Liu, M. and Wang, S., J. Comput. Aid.Mol. Des., 13 (1999) 435.

    Google Scholar 

  13. Wang, J.W., Kollman, P.A. and Kuntz, I.D., Proteins, 36 (1999) 1.

    PubMed  Google Scholar 

  14. Jones, G., Willett, P. and Glen, R.C., J. Mol. Biol., 245 (1995) 43.

    PubMed  Google Scholar 

  15. MacKerell, Jr., A.D., Bashford, D., Bellott, M., Dunbrack Jr., R.L., Evanseck, J.D., Field, M.J., Fischer, S., Gao, J., Guo, H., Ha, S., Joseph-McCarthy, D., Kuchnir, L., Kuczera, K., Lau, F.T.K., Mattos, C.; Michnick, S., Ngo, T., Nguyen, D.T., Prodhom, B., Reiher, III, W.E., Roux, B., Schlenkrich, M., Smith, J.C., Stote, R. Straub, J., Watanabe, M., Wiorkiewicz-Kuczera, J., Yin, D. and Karplus, M., J. Phys. Chem. B102 (1998) 3586.

    Google Scholar 

  16. The QUANTA Molecular Modeling Program. Molecular Simulation, Incorporated.

  17. Pattabiraman, N., Levitt, M., Ferring T.E. and Langridge, R., J. Comput. Chem., 6 (1985) 432.

    Google Scholar 

  18. Given, J.A. and Gilson, M.K., Proteins, 33 (1998) 475.

    PubMed  Google Scholar 

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

    PubMed  Google Scholar 

  20. Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N. and Bourne, P.E., Nucl. Acids Res., 28 (2000) 235.

    PubMed  Google Scholar 

  21. Burmeister, W.P., Henrissat, B., Bosso, C., Cusack, S. and Ruigrok, R.W.H., Structure, 1 (1993) 19.

    PubMed  Google Scholar 

  22. Brandstetter, H., Turk, D., Hoeffken, H.W., Grosse, D., Stuerzebecher, J., Martin, P.D., Edwards, B.F.P. and Bode, W., J. Mol. Biol., 226 (1992) 1085.

    PubMed  Google Scholar 

  23. Bolin, J.T., Filman, D.J., Matthews, D.A., Hamlin, R.C. and Kraut, J., J. Biol. Chem. 257 (1999) 13650.

    Google Scholar 

  24. Lam, P., Jadhav, P., Eyermann, C., Hodge, N., Ru, Y., Bacheler, L., Meek, J., Otto, M., Rayner, M., Wong, Y., Chang, C.-H., Weber, P., Jackson, D., Sharpe, T. and Erickson-Viitanen, S., Science, 263 (1994) 380.

    PubMed  Google Scholar 

  25. Marquart, M., Walter, J., Deisenhofer, J., Bode, W. and Huber, R., Acta Crystallogr., B39 (1983) 480.

    Google Scholar 

  26. Abad-Zapatero, C., Griffith, J.P., Sussman, J.L. and Rossmann, M.G., J. Mol. Biol., 198 (1987) 445.

    PubMed  Google Scholar 

  27. Poulos, T.L., Finzel, B.C. and Howard, A.J., J. Mol. Biol., 87 (1987) 687.

    Google Scholar 

  28. Padlan, E.A., Cohen, G.H. and Davies, D.R., Ann. Inst. Pasteur Immunol., 136 (1985) 271.

    Google Scholar 

  29. Weber, P.C., Ohlendorf, D.H., Wendoloski, J.J. and Salemme, F.R., Science, 243 (1989) 85.

    PubMed  Google Scholar 

  30. Christianson, D.W. and Lipscomb, W.N., Proc. Natl. Acad. Sci. USA, 83 (1986) 7568.

    PubMed  Google Scholar 

  31. Krengel, U., Schlichting, I., Scheidig, A., Frech, M., John, J. Lautwein, A., Wittinghofer, F., Kabsch, W. and Pai, E.F., Nato Asi Ser., A220 (1991) 183.

    Google Scholar 

  32. Weis, W.I., Bruenger, A.T., Skehel, J.J. and Wiley, D.C., J. Mol. Biol., 212 (1990) 737.

    PubMed  Google Scholar 

  33. Monzingo, A.F. and Matthews, B.W., Biochemistry, 23 (1984) 5724.

    PubMed  Google Scholar 

  34. Bone, R., Vacca, J.P., Anderson, P.S. and Holloway, M.K., J. Am. Chem. Soc., 113 (1991) 9382.

    Google Scholar 

  35. Baldwin, E.T., Bhat, T.N., Gulnik, S., Liu, B., Topol, I.A., Kiso, Y., Mimoto, T., Mitsuya, H. and Erickson, J.W., Structure, 3 (1995) 581.

    PubMed  Google Scholar 

  36. Bocskei, Z., Groom, C.R., Flower, D.R., Wright, C.E., Phillips, S.E.V., Cavaggioni, A., Findlay, J.B.C. and North, A.C.T., Nature, 360 (1992) 186.

    PubMed  Google Scholar 

  37. Edmundson, A.B., Harris, D.L., Fan, Z.-C., Guddat, L.W., Schley, B.T., Hanson, B.L., Tribbick, G. and Geysen, H.M., Proteins Struct. Funct. Genet., 16 (1993) 246.

    PubMed  Google Scholar 

  38. Perry, K.M., Carreras, C.W., Chang, L.C., Santi, D.V. and Stroud, R.M., Biochemistry, 32 (1993) 7116.

    PubMed  Google Scholar 

  39. Hamilton, J.A., Steinrauf, L.K., Braden, B.C., Liepnieks, J.J., and Benson, M.D., J. Biol. Chem., 268 (1993) 2416.

    PubMed  Google Scholar 

  40. Oren, D.A., Jacobo-Molina, A., Williams, R.L., Kamer, G., Rubenstein, D.A., Li, Y., Rozhon, E., Cox, S., Buontempo, P., O'Connell, J., Schwartz, J., Miller, G., Bauer, B., Versace, R., Pinto, P., Ganguly, A., Girijavallabhan, V. and Arnold, E., J. Mol. Biol., 230 (1993) 857.

    PubMed  Google Scholar 

  41. Harel, M., Schalk, I., Ehret-Sabattier, L., Bouet, F., Goeldner, M., Hirth, C., Axelsen, P., Silman, I. and Sussman, J., Proc. Natl. Acad. Sci. USA, 90 (1993) 9031.

    PubMed  Google Scholar 

  42. Eads, J.C., Sacchettini, J.C., Komminga, A. and Gordon, J.I., Cell, 78 (1994) 325.

    PubMed  Google Scholar 

  43. Lalonde, J.M., Bernlohr, D.A. and Banaszak, L.J., Biochemistry, 33 (1994) 4885.

    PubMed  Google Scholar 

  44. Dreyer, G.B., Lambert, D.M., Meek, T.D., Carr, T.J., Tomaszek, Jr. T.A., Fernandez, A.V., Bartus, H., Cacciavillani, E., Hassell, A.M., Minnich, M., Petteway, S.R., and Metcalf, B.W., Biochemistry, 31 (1992) 6646.

    PubMed  Google Scholar 

  45. Brooks, B.R., Bruccoleri, R.E., Olafson, B.D., States, D.J., Swaminathan S. and Karplus, M., J. Comput. Chem., 4 (1983) 187.

    Google Scholar 

  46. Hardy, L.W., Finer-Moore, J.S., Montfort, W.R., Jones, M.O., Santi, D.V. and Stroud, R.M., Science, 235 (1987) 448.

    PubMed  Google Scholar 

  47. Jones, G., Willett, P. and Glen, R.C., Leach, A.R., and Taylor, R., J. Mol. Biol., 207 (1997) 727.

    Google Scholar 

  48. Gehlhaar, D.G., Verkhivker, G.M., Rejto, P.A., Sherman, C.J., Fogel, D.B., Fogel, L.J. and Freer, S.T., Chem. Biol., 2 (1995) 317.

    PubMed  Google Scholar 

  49. Jano, I., Compt. Rend. Acad. Sci. Paris, 261 (1965) 103.

    Google Scholar 

  50. David, L., Luo, R. and Gilson, M.K., J. Phys. Chem. A 103 (1999) 1031.

    Google Scholar 

  51. Kramer, B., Rarey, M. and Lengauer, T., Proteins Struct. Funct. Genet., 37 (1999) 228.

    PubMed  Google Scholar 

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  1. Center for Advanced Research in Biotechnology, 9600 Gudelsky Drive, Rockville, MD, 20850, USA

    Laurent David, Ray Luo & Michael K. Gilson

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  1. Laurent David
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  2. Ray Luo
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David, L., Luo, R. & Gilson, M.K. Ligand-receptor docking with the Mining Minima optimizer. J Comput Aided Mol Des 15, 157–171 (2001). https://doi.org/10.1023/A:1008128723048

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