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


BACKGROUND
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.
von Grotthuss
Marcin
M
BioInfoBank Institute, ul. Limanowskiego 24A, 60-744 Poznan, Poland. leszek@bioinfo.pl
Pas
Jakub
J
Rychlewski
Leszek
L
D001665:Binding Sites; D003196:Computer Graphics; D017124:Conserved Sequence / Q000235:genetics; D003628:Database Management Systems; D030562:Databases, Protein; D020869:Gene Expression Profiling / Q000379:methods; D023281:Genomics / Q000379:methods; D016247:Information Storage and Retrieval / Q000379:methods; D011485:Protein Binding; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry* / Q000235:genetics; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods; D017385:Sequence Homology; D012984:Software; D014584:User-Computer Interface
D011506:Proteins