Skip to main content
Log in

Filtering databases and chemical libraries

  • Published:
Journal of Computer-Aided Molecular Design Aims and scope Submit manuscript

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

References

  1. Thorpe, D.S., Chan, A.W.E., Binnie, A., Chen, L.C., Robinson, A., Spoonamore, J., Rodwell, D., Wade, S., Wilson, S., Ackerman-Berrier, M., Yeoman, H., Walle, S., Wu, Q., Wertman, K.F., Biochem. Biophys. Res. Commun., 266 (1999) 62–65.

    Google Scholar 

  2. Weininger, D., J. Chem. Inf. Comput. Sci., 28 (1988) 31–36.

    Google Scholar 

  3. Weininger, D., Weininger, A. and Weininger, J.L., J. Chem. Inf. Comput. Sci., 29 (1989) 97–101.

    Google Scholar 

  4. Lipinski, C.A., Lombardo, F., Dominy, B.W. and Feeney, P.J., Adv. Drug Delivery Rev., 23 (1997) 3–25.

    Google Scholar 

  5. Ghose, A.K., Viswanadhan, V.N. and Wendelowski, J.J., J. Comb. Chem., 1 (1999) 55–67.

    Google Scholar 

  6. Ghose, A.K., Viswanadhan, V.N. and Wendoloski, J.J., J. Phys. Chem. A., 102 (1998) 3762–3772.

    Google Scholar 

  7. Oprea, T.I., J. Comput. Aided Mol. Des., 14 (2000) 251–264.

    Google Scholar 

  8. Lipinski, C.A., J Pharmacol. Toxicol. Methods, 44 (2000) 235–249.

    Google Scholar 

  9. Oprea, T.I., Davis, A.M., Teague, S.J. and Leeson, P.D., J. Chem. Inf. Comput. Sci., (2001)

  10. Hann, M.M., Leach, A.R. and Harper, G., J. Chem. Inf. Comput. Sci., 41 (2001) 856–864.

    Google Scholar 

  11. Hann, M., Hudson, B., Lewell, X., Lifely, R., Miller, L. and Ramsden, N., J. Chem. Inf. Comput. Sci., 39 (1999) 897–902.

    Google Scholar 

  12. Leach, A.R., Bradshaw, J., Green, D.V.S., Hann, M.M. and Delany, III, J.J., J. Chem. Inf. Comput. Sci., (1999) 1161–1172.

  13. Rishton, G.M., Drug Discovery Today, 2 (1997) 382–385.

    Google Scholar 

  14. Kuntz, I.D., Chen, K., Sharp, K.A. and Kollman, P.A., Proc. Natl. Acad. Sci. USA, 96 (1999) 9997–10002.

    Google Scholar 

  15. James, C.A., Weininger, D. and Delany, J., Daylight Theory Manual, http://www.daylight.com/dayhtml/ doc/theory/theory.smarts.html

  16. Unity, Tripos, St. Louis, MO, http://www.tripos.com

  17. Molecular Operating Environment, Chemical Computing Group, Montreal, Quebec, Canada, http:// www.chemcomp.com

  18. Ajay, Bemis, G.W. and Murcko, M.A., J. Med. Chem., (1999) 4942–4951.

  19. March, J., Advanced Organic Chemistry: Reactions, Mechanisms, and Structure, John Wiley & Sons, 1992

  20. Andrews, P.R., Craik, D.J. and Martin, J.L., J. Med. Chem., 27 (1984) 1648–1657.

    Google Scholar 

  21. Muegge, I., Heald, S.L. and Brittelli, D., J. Med. Chem., 44 (2001) 1841–1846.

    Google Scholar 

  22. Barnard, J.M., Downs, G.A., von Scholley-Pfab, A. and Brown, R.D., J. Mol. Graph. Model., 18 (2000) 452–463.

    Google Scholar 

  23. Shi, S., Peng, Z., Kostrowicki, J., Paderes, G. and Kuki, A., J. Mol. Graph. Model., 18 (2000) 478–496.

    Google Scholar 

  24. Weiss, S.M. and Kulikowski, C.A., Computer Systems That Learn, Morgan Kaufmann, 1991.

  25. Mitchell, T.M., Machine Learning, McGraw Hill, 1997.

  26. Ajay, Walters, W.P. and Murcko, M.A., J. Med. Chem., 41 (1998) 3314–3324.

    Google Scholar 

  27. Wagener, M. and van Geerestein, V.J., J. Med. Chem., 40 (2000) 280–292.

    Google Scholar 

  28. Quinlan, J.R., C4.5: Programs for Machine Learning, Morgan Kaufmann, 1993.

  29. Sadowski, J. and Kubinyi, H., J.Med. Chem., 41 (1998) 3325–3329.

    Google Scholar 

  30. Stahl, M. and Rarey, M., J. Med. Chem., 44 (2001) 1035–1042.

    Google Scholar 

  31. Charifson, P.S., Corkery, J.J., Murcko, M.A. and Walters, W.P., J Med Chem, 42 (1999) 5100–5109.

    Google Scholar 

  32. Muegge, I. and Martin, Y.C., J. Med. Chem., 42 (1999) 791–804.

    Google Scholar 

  33. Meng, E.C., Shoichet, B.K. and Kuntz, I.D., J. Comp. Chem., 13 (1992) 505–524.

    Google Scholar 

  34. Shoichet, B.K., Stroud, R.M., Santi, D.V., Kuntz, I.D. and Perry, K.M., Science, 259 (1993) 1445–1450.

    Google Scholar 

  35. Kuntz, I.D., Blaney, J.M., Oatley, S.J., Langridge, R. and Ferrin, T.E., J. Molec. Biol., 161 (1982) 269–288.

    Google Scholar 

  36. DesJarlais, R.L., Sheridan, R.P., Seibel, G.L., Dixon, J.S., Kuntz, I.D. and Venkataraghavan, R., J. Med. Chem., 31 (1988) 722–729.

    Google Scholar 

  37. Shoichet, B.K., Bodian, D.L. and Kuntz, I.D., J. Comp. Chem., 13 (1992) 380–397.

    Google Scholar 

  38. Stahl, M. and Bohm, H.J., J. Mol. Graph. Model., 16 (1998) 121–132.

    Google Scholar 

  39. PDB refcode 2PRG

  40. Gehlhaar, D.K., Verkhivker, G.M., Rejto, P.A., Sherman, C.J., Fogel, D.B. and Freer, S.T., Chem. Bio., 2 (1995) 317–324.

    Google Scholar 

  41. Böhm, H.-J., J. Comput.-Aided Mol. Design, 12 (1998) 309–323.

    Google Scholar 

  42. First Discovery Technical Notes Manual, version 1.8, Schrodinger, Inc., New York, NY

  43. Eldridge, M.D., Murray, C.W., Auton, T.R., Paolini, G.V. and Mee, R.PP., J. Comput.-Aided Mol. Design, 11 (1997) 425–445.

    Google Scholar 

  44. Volter, K.E., Embrey, K.J., Pierens, G.K. and Quinn, R.J., Eur J Pharm Sci, 12 (2001) 181–194.

    Google Scholar 

  45. Clark, D.E., Westhead, D.R., Sykes, R.A. and Murray, C.W., J. Comput.-Aided Mol Des, 10 (1996) 397–416.

    Google Scholar 

  46. Moro, S., Li, A.H. and Jacobson, K.A., J. Chem. Inf. Comput. Sci., 38 (1998) 1239–1248.

    Google Scholar 

  47. Murray, C.M. and Cato, S.J., J. Chem. Inf. Comput. Sci., 39 (1999) 46–50.

    Google Scholar 

  48. Mason, J.S., Morize, I., Menard, P.R., Cheney, D.L., Hulme, C. and Labaudiniere, R.F., J. Med. Chem., 42 (1999) 3251–3264.

    Google Scholar 

  49. Mason, J.S. and Cheney, D.L., Pac. Symp. Biocomput., (2000) 576–587.

  50. VIDA, OpenEye Scientific Software, Santa Fe, NM, http://www.eyesopen.com

  51. FRED, OpenEye Scientific Software, Sante Fe, NM, http://www.eyesopen.com

  52. Pearlman, D.A. and Walters, W.P., manuscript in preparation.

Download references

Author information

Authors and Affiliations

Authors

Rights and permissions

Reprints and permissions

About this article

Cite this article

Charifson, P.S., Walters, W.P. Filtering databases and chemical libraries. J Comput Aided Mol Des 16, 311–323 (2002). https://doi.org/10.1023/A:1020829519597

Download citation

  • Issue Date:

  • DOI: https://doi.org/10.1023/A:1020829519597

Keywords

Navigation