Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Commentary
  • Published:

Systems chemical biology

Nature Chemical Biology volume 3, pages 447–450 (2007)Cite this article

The increasing availability of data related to genes, proteins and their modulation by small molecules has provided a vast amount of biological information leading to the emergence of systems biology and the broad use of simulation tools for data analysis. However, there is a critical need to develop cheminformatics tools that can integrate chemical knowledge with these biological databases and simulation approaches, with the goal of creating systems chemical biology.

This is a preview of subscription content, access via your institution

Relevant articles

Open Access articles citing this article.

Access options

Buy this article

  • Purchase on SpringerLink
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1: A simplified representation of the glyoxylate pathway, extracted from KEGG.
Figure 2: Conceptual representation of the systems chemical biology approach, applied to the glyoxylate pathway.

References

  1. Voit, E., Neves, A.R. & Santos, H. Proc. Natl. Acad. Sci. USA 103, 9452–9457 (2006).

    Article  CAS  Google Scholar 

  2. Kell, D.B. FEBS J. 273, 873–894 (2006).

    Article  CAS  Google Scholar 

  3. Blinov, M.L., Faeder, J.R., Goldstein, B. & Hlavacek, W.S. Biosystems 83, 136–151 (2006).

    Article  CAS  Google Scholar 

  4. Ochi, H. & Westerfield, M. Dev. Growth Differ. 49, 1–11 (2007).

    Article  CAS  Google Scholar 

  5. Brandman, O., Ferrell, J.E., Li, R. & Meyer, T. Science 310, 496–498 (2005).

    Article  CAS  Google Scholar 

  6. Covert, M.W., Knight, E.M., Reed, J.L., Herrgard, M.J. & Palsson, B.O. Nature 429, 92–96 (2004).

    Article  CAS  Google Scholar 

  7. Keiser, M.J. et al. Nat. Biotechnol. 25, 197–206 (2007).

    Article  CAS  Google Scholar 

  8. Morphy, R. & Rankovic, Z. Drug Discov. Today 12, 156–160 (2007).

    Article  CAS  Google Scholar 

  9. Loging, W., Harland, L. & Williams-Jones, B. Nat. Rev. Drug Discov. 6, 220–230 (2007).

    Article  CAS  Google Scholar 

  10. Austin, C.P., Brady, L.S., Insel, T.R. & Collins, F.S. Science 306, 1138–1139 (2004).

    Article  CAS  Google Scholar 

  11. Brown, F. Curr. Opin. Drug Discov. Devel. 8, 298–302 (2005).

    CAS  PubMed  Google Scholar 

  12. Olsson, T. & Oprea, T.I. Curr. Opin. Drug Discov. Devel. 4, 308–313 (2001).

    CAS  PubMed  Google Scholar 

  13. Willett, P. Aslib Proc. (in the press).

  14. Paolini, G.V., Shapland, R.H.B., van Hoorn, W.P., Mason, J.S. & Hopkins, A.L. Nat. Biotechnol. 24, 805–815 (2006).

    Article  CAS  Google Scholar 

  15. Fliri, A.F., Loging, W.T., Thadeio, P.F. & Volkmann, R.A. Proc. Natl. Acad. Sci. USA 102, 261–266 (2005).

    Article  CAS  Google Scholar 

  16. Anonymous. Technology Review, published online September 2001 http://www.technologyreview.com/Biotech/12575.

  17. Schreiber, S.L. Nat. Chem. Biol. 1, 64–66 (2005).

    Article  CAS  Google Scholar 

  18. Tropsha, A. in Comprehensive Medicinal Chemistry II Vol. 4 (ed. Mason, J.) 149–165 (Elsevier, Oxford, UK, 2006).

    Google Scholar 

  19. Fara, D.C. et al. Drug Discov. Today Technol. 3, 377–385 (2006).

    Article  Google Scholar 

  20. Oprea, T.I. & Tropsha, A. Drug Discov. Today Technol. 3, 357–365 (2006).

    Article  Google Scholar 

  21. Roth, B.L. & Kroeze, W.K. Curr. Pharm. Des. 12, 1785–1795 (2006).

    Article  CAS  Google Scholar 

  22. Burchiel, S.W., Thompson, T.A., Lauer, F.T. & Oprea, T.I. Toxicol. Appl. Pharmacol. 221, 203–214 (2007).

    Article  CAS  Google Scholar 

  23. Martin, S., Davidson, G., May, E., Faulon, J.-L. & Werner-Washburne, M. in Proc. IEEE Comput. Syst. Bioinform. Conf., Stanford, California, USA, 16–19 August 2004 (ed. Markstein, V.) 566–569 (IEEE Computer Society, Los Alamitos, California, USA, 2004).

    Google Scholar 

  24. Schiek, R.L. & May, E.E. in Proc. IEEE Comput. Syst. Bioinform. Conf., Stanford, California, USA, 11–14 August 2003 (ed. Markstein, V.) 620–622 (IEEE Computer Society, Los Alamitos, California, USA, 2003).

    Google Scholar 

  25. Schomburg, I. et al. Nucleic Acids Res. 32, D431–D433 (2004).

    Article  CAS  Google Scholar 

  26. Borgwardt, K.M. et al. Bioinformatics 21 (suppl. 1), i47–i56 (2005).

    Article  CAS  Google Scholar 

  27. Cai, C.Z., Han, L.Y., Ji, Z.L., Chen, X. & Chen, Y.Z. Nucleic Acids Res. 31, 3692–3697 (2003).

    Article  CAS  Google Scholar 

  28. Kunik, V., Solan, Z., Edelman, S., Ruppin, E. & Horn, D. in Proc. IEEE Comput. Syst. Bioinform. Conf., Stanford, California, USA, 8–11 August 2004 (ed. Markstein, V.) 80–85 (IEEE Computer Society, Los Alamitos, California, USA, 2005).

    Google Scholar 

  29. Kalinina, O.V., Novichkov, P.S., Mironov, A.A., Gelfand, M.S. & Rakhmaninova, A.B. Nucleic Acids Res. 32, W424–W428 (2004).

    Article  CAS  Google Scholar 

  30. Oprea, T.I. & Matter, H. Curr. Opin. Chem. Biol. 8, 349–358 (2004).

    Article  CAS  Google Scholar 

  31. Latino, D.A.R.S. & Aires-de-Sousa, J. Angew. Chem. Int. Ed. 45, 2066–2069 (2006).

    Article  CAS  Google Scholar 

  32. Gasteiger, J. J. Comput. Aided Mol. Des. 21, 33–52 (2007).

    Article  CAS  Google Scholar 

  33. Kotera, M., Okuno, Y., Hattori, M., Goto, S. & Kanehisa, M. J. Am. Chem. Soc. 126, 16487–16498 (2004).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

Download references

Acknowledgements

This work was supported in part by the NIH grant U54 MH074425-01 (T.I.O.) and by the NIH planning grant P20-HG003898 (A.T.). Sandia is operated by Sandia Corporation, a Lockheed Martin Company, for the US Department of Energy under Contract DE-AC04-94AL85000 (J.-L.F. and M.D.R.). The authors express their gratitude to T.K. Allu and D.C. Fara (University of New Mexico) for the PubChem bioassay data analysis.

Author information

Authors and Affiliations

  1. Tudor I. Oprea is in the Division of Biocomputing, MSC11 6145, University of New Mexico School of Medicine, 2703 Frontier NE, Albuquerque, New Mexico 87131, USA. toprea@salud.unm.edu,

    Tudor I Oprea

  2. Alexander Tropsha is in the Laboratory for Molecular Modeling, CB # 7360 Beard Hall, School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA.,

    Alexander Tropsha

  3. Jean-Loup Faulon and Mark D. Rintoul are at Sandia National Laboratories, PO Box 5800, Albuquerque, New Mexico 87185, USA.,

    Jean-Loup Faulon & Mark D Rintoul

Authors
  1. Tudor I Oprea
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Alexander Tropsha
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Jean-Loup Faulon
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Mark D Rintoul
    View author publications

    You can also search for this author in PubMed Google Scholar

Ethics declarations

Competing interests

T.I.O. is the founder and CEO of Sunset Molecular Discovery LLC, which markets small-molecule databases for the pharmaceutical industry. He also serves on the Scientific Advisory Board for ChemDiv, Inc., and he owns stock in AstraZeneca plc.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Oprea, T., Tropsha, A., Faulon, JL. et al. Systems chemical biology. Nat Chem Biol 3, 447–450 (2007). https://doi.org/10.1038/nchembio0807-447

Download citation

  • Issue Date:

  • DOI: https://doi.org/10.1038/nchembio0807-447

This article is cited by

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing