Skip to main content

CLEVER: A General Design Tool for Combinatorial Libraries

  • Protocol
  • First Online:
  • 1423 Accesses

Part of the book series: Methods in Molecular Biology ((MIMB,volume 685))

Abstract

CLEVER is a computational tool designed to support the creation, manipulation, enumeration, and visualization of combinatorial libraries. The system also provides a summary of the diversity, coverage, and distribution of selected compound collections. When deployed in conjunction with large-scale virtual screening campaigns, CLEVER can offer insights into what chemical compounds to synthesize, and, more importantly, what not to synthesize. In this chapter, we describe how CLEVER is used and offer advice in interpreting the results.

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

Buying options

Protocol
USD   49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   89.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   119.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD   169.99
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

Learn about institutional subscriptions

Springer Nature is developing a new tool to find and evaluate Protocols. Learn more

References

  1. Martin, E. J., Critchlow, R. E. (1999) Beyond mere diversity: tailoring combinatorial libraries for drug discovery. J Comb Chem 1, 32–45.

    Article  CAS  PubMed  Google Scholar 

  2. Valler, M. J., Green, D. (2000) Diversity screening versus focussed screening in drug discovery. Drug Discov Today 5, 286–293.

    Article  PubMed  Google Scholar 

  3. Jamois, E. A. (2003) Reagent-based and product-based computational approaches in library design. Curr Opin Chem Biol 7, 326–330.

    Article  CAS  PubMed  Google Scholar 

  4. Leach, A. R., Hann, M. M. (2000) The in silico world of virtual libraries. Drug Discov Today 5, 326–336.

    Article  CAS  PubMed  Google Scholar 

  5. Schüller, A., Hähnke, V., Schneider, G. (2007) SmiLib v2.0: a Java-based tool for rapid combinatorial library enumeration. QSAR Comb Sci 26, 407–410.

    Article  Google Scholar 

  6. Weininger, D. (1988) SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules. J Chem Inf Comput Sci 28, 31–36.

    Article  CAS  Google Scholar 

  7. Steinbeck, C., Hoppe, C., Kuhn, S., Floris, M., Guha, R., Willighagen, E. L. (2006) Recent developments of the chemistry development kit (CDK)—an open-source java library for chemo- and bioinformatics. Curr Pharm Des 12, 2111–2120.

    Article  CAS  PubMed  Google Scholar 

  8. Guha, R., Howard, M. T., Hutchison, G. R., Murray-Rust, P., Rzepa, H., Steinbeck, C., Wegner, J., Willighagen, E. L. (2006) The Blue Obelisk—interoperability in chemical informatics. J Chem Inf Model 46, 991–998.

    Article  CAS  PubMed  Google Scholar 

  9. Sadowski, J. (1997) A hybrid approach for addressing ring flexibility in 3D database searching. J Comput Aided Mol Des 11, 53–60.

    Article  CAS  PubMed  Google Scholar 

  10. Angel, H. (2006) Biomolecules in the computer: Jmol to the rescue. Biochem Educ 34, 255–261.

    Article  Google Scholar 

  11. Rickards, R. W., Rothschild, J. M., Willis, A. C., de Chazal, N. M., Kirk, J., Kirk, K., Saliba, K. J., Smith, G. D. (1999) Calothrixins A and B, novel pentacyclic metabolites from Calothrix Cyanobacteria with potent activity against malaria parasites and human cancer cells. Tetrahedron Lett 55, 13513–13520.

    CAS  Google Scholar 

  12. Bernardo, P. H., Chai, C. L. L., Heath, G. A., Mahon, P. J., Smith, G. D., Waring, P., Wilkes, B. A. (2004) Synthesis, electrochemistry, and bioactivity of the Cyanobacterial Calothrixins and related quinones. J Med Chem 47, 4958–4963.

    Article  CAS  PubMed  Google Scholar 

  13. Bernardo, P. H., Chai, C. L. L., Le Guen, M.,Geoffrey D., Smith, G. D., Waring, P. (2006) Structure–activity delineation of quinones related to the biologically active Calothrixin B. Bioorg Med Chem Lett 17, 82–85.

    Article  PubMed  Google Scholar 

  14. Khan, Q. A., Lu, J., Hecht, S. M. (2009) Calothrixins, A new class of human DNA topoisomerase I poisons. J Nat Prod 72, 438–442.

    Article  CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2011 Springer-Science+Business Media, LLC

About this protocol

Cite this protocol

Lam, T.H., Bernardo, P.H., Chai, C.L., Tong, J.C. (2011). CLEVER: A General Design Tool for Combinatorial Libraries. In: Zhou, J. (eds) Chemical Library Design. Methods in Molecular Biology, vol 685. Humana Press. https://doi.org/10.1007/978-1-60761-931-4_18

Download citation

  • DOI: https://doi.org/10.1007/978-1-60761-931-4_18

  • Published:

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-60761-930-7

  • Online ISBN: 978-1-60761-931-4

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics