Skip to main content

Computer Aided Rational Design of Biochemical Systems

  • Conference paper
  • First Online:
Animal Cell Technology: Basic & Applied Aspects

Part of the book series: Animal Cell Technology: Basic & Applied Aspects ((ANICELLTECH,volume 16))

  • 1046 Accesses

Abstract

To rationally design biological networks at the molecular interaction level, computer-aided design (CAD) is a promising technology, which is based on analogy to engineering technology. CADLIVE (Computer-Aided Design of LIVing systEms) is a comprehensive software suit that consists of multiple modules: a GUI-supported network designer, a database, an automatic layout application, and a dynamic simulator. The most advantageous feature is that the employed regulator-reaction equations connect these applications directly. Once a biochemical network map is provided, CADLIVE efficiently analyzes its static and dynamic features. It is one of the most advanced and integrative bio-simulators.

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

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 259.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 329.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 329.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Nishio, Y., Usuda, Y., Matsui, K., and Kurata, H. (2008) Computer-aided rational design of the phosphotransferase system for enhanced glucose uptake in Escherichia coli. Mol. Syst. Biol. 4: 160.

    Article  PubMed  Google Scholar 

  2. Kurata, H., Matoba, N., and Shimizu, N. (2003) CADLIVE for constructing a large-scale biochemical network based on a simulation-directed notation and its application to yeast cell cycle. Nucleic Acids Res. 31: 4071–4084.

    Article  CAS  PubMed  Google Scholar 

  3. Kurata, H., Inoue, K., Maeda, K., Masaki, K., Shimokawa, Y., et al. (2007) Extended CADLIVE: A novel graphical notation for design of biochemical network maps and computational pathway analysis. Nucleic Acids Res. 35: e134.

    Article  PubMed  Google Scholar 

  4. Li, W. and Kurata, H. (2005) A grid layout algorithm for automatic drawing of biochemical networks. Bioinformatics 21: 2036–2042.

    Article  CAS  PubMed  Google Scholar 

  5. Kurata, H., Masaki, K., Sumida, Y., and Iwasaki, R. (2005) CADLIVE dynamic simulator: Direct link of biochemical networks to dynamic models. Genome Res. 15: 590–600.

    Article  CAS  PubMed  Google Scholar 

  6. Kohn, K.W. (1999) Molecular interaction map of the mammalian cell cycle control and DNA Repair systems. Mol. Biol. Cell 10: 2703–2734.

    CAS  PubMed  Google Scholar 

  7. Ninfa, A.J., Jiang P., Atkinson M.R., and Peliska J.A. (2000) Integration of antagonistic signals in the regulation of nitrogen assimilation in Escherichia coli. Curr. Top. Cell Regul. 36: 31–75.

    Article  CAS  PubMed  Google Scholar 

  8. Ninfa, A.J. and Atkinson, M.R. (2000) PII signal transduction proteins. Trends Microbiol. 8: 172–179.

    Article  CAS  PubMed  Google Scholar 

  9. Blauwkamp, T.A. and Ninfa, A.J. (2002) Physiological role of the GlnK signal transduction protein of Escherichia coli: Survival of nitrogen starvation. Mol. Microbiol. 46: 203–214.

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

This work was supported by KAKENHI (Grant-in-Aid for Scientific Research) on Priority Areas “Systems Genomics” from the Ministry of Education, Culture, Sports, Science and Technology of Japan and partially by KAKENHI (Grant-in-Aid for Scientific Research (B), 2006, 18300098).

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Hiroyuki Kurata .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2010 Springer Science+Business Media B.V.

About this paper

Cite this paper

Kurata, H. (2010). Computer Aided Rational Design of Biochemical Systems. In: Kamihira, M., Katakura, Y., Ito, A. (eds) Animal Cell Technology: Basic & Applied Aspects. Animal Cell Technology: Basic & Applied Aspects, vol 16. Springer, Dordrecht. https://doi.org/10.1007/978-90-481-3892-0_2

Download citation

Publish with us

Policies and ethics