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Bioinformatics Vol. 19 no. 8 2003
Pages 1041-1042
© 2003 Oxford University Press

Applications Note

Ligand-Info, searching for similar small compounds using index profiles

Marcin von Grotthuss , Jakub Pas and Leszek Rychlewski *

BioInfoBank Institute, ul. Limanowskiego 24A, 60-744 Poznan, Poland

Received on July 19, 2002 ; revised on October 11, 2002 and December 12, 2002 ; accepted on December 20, 2002

Motivation: The Ligand-Info system is based on the assumption that small molecules with similar structure have similar functional (binding) properties. The developed system enables a fast and sensitive index based search for similar compounds in large databases. Index profiles, constructed by averaging indexes of related molecules are used to increase the specificity of the search. The utilization of index profiles helps to focus on frequent, common features of a family of compounds.

Results: A Java-based tool for clustering and scanning of small molecules has been created. The tool can interactively cluster sets of molecules and create index profiles on the user side and automatically download similar molecules from a databases of 250 000 compounds. The results of the application of index profiles demonstrate that the profile based search strategy can increase the quality of the selection process.

Availability: The system is available at http://Ligand.Info. The application requires the Java Runtime Environment 1.4, which can be automatically installed during the first use on desktop systems, which support it. A standalone version of the program is available from the authors upon request.

Contact: leszek{at}bioinfo.pl

* To whom correspondence should be addressed.


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