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
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsReferences
Martin, E. J., Critchlow, R. E. (1999) Beyond mere diversity: tailoring combinatorial libraries for drug discovery. J Comb Chem 1, 32–45.
Valler, M. J., Green, D. (2000) Diversity screening versus focussed screening in drug discovery. Drug Discov Today 5, 286–293.
Jamois, E. A. (2003) Reagent-based and product-based computational approaches in library design. Curr Opin Chem Biol 7, 326–330.
Leach, A. R., Hann, M. M. (2000) The in silico world of virtual libraries. Drug Discov Today 5, 326–336.
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.
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.
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.
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.
Sadowski, J. (1997) A hybrid approach for addressing ring flexibility in 3D database searching. J Comput Aided Mol Des 11, 53–60.
Angel, H. (2006) Biomolecules in the computer: Jmol to the rescue. Biochem Educ 34, 255–261.
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.
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.
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.
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.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights 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