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SuperTarget and Matador: resources for exploring drug-target relationships.

Günther S, Kuhn M, Dunkel M, Campillos M, Senger C, Petsalaki E, Ahmed J, Urdiales EG, Gewiess A, Jensen LJ, Schneider R, Skoblo R, Russell RB, Bourne PE, Bork P, Preissner R - Nucleic Acids Res. (2007)

Bottom Line: Therefore, we developed a one-stop data warehouse, SuperTarget that integrates drug-related information about medical indication areas, adverse drug effects, drug metabolization, pathways and Gene Ontology terms of the target proteins.The database contains more than 2500 target proteins, which are annotated with about 7300 relations to 1500 drugs; the vast majority of entries have pointers to the respective literature source.A subset of these drugs has been annotated with additional binding information and indirect interactions and is available as a separate resource called Matador.

View Article: PubMed Central - PubMed

Affiliation: Structural Bioinformatics Group, Institute of Molecular Biology and Bioinformatics, Charité-University Medicine Berlin, Arnimallee 22, 14195 Berlin, Germany.

ABSTRACT
The molecular basis of drug action is often not well understood. This is partly because the very abundant and diverse information generated in the past decades on drugs is hidden in millions of medical articles or textbooks. Therefore, we developed a one-stop data warehouse, SuperTarget that integrates drug-related information about medical indication areas, adverse drug effects, drug metabolization, pathways and Gene Ontology terms of the target proteins. An easy-to-use query interface enables the user to pose complex queries, for example to find drugs that target a certain pathway, interacting drugs that are metabolized by the same cytochrome P450 or drugs that target the same protein but are metabolized by different enzymes. Furthermore, we provide tools for 2D drug screening and sequence comparison of the targets. The database contains more than 2500 target proteins, which are annotated with about 7300 relations to 1500 drugs; the vast majority of entries have pointers to the respective literature source. A subset of these drugs has been annotated with additional binding information and indirect interactions and is available as a separate resource called Matador. SuperTarget and Matador are available at http://insilico.charite.de/supertarget and http://matador.embl.de.

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Example of a complex query: search for an alternative drug to Taxol, which adresses the same target Bcl-2, but is not metabolized by the cytochrome 2C8. Procedure: start to search for the targets and the metabolizing cytochromes of Taxol in the associated categories. The resulting lists contain among others the target Bcl-2 as well as the P450 cytochrome 2C8. Second, forward 2C8 and Bcl-2 into the query term box, combine them using the ‘NOT’ operator and submit the query. The resulting drug list contains two alternative drug candidates for Taxol (Docetaxel and Flupirtine).
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Figure 2: Example of a complex query: search for an alternative drug to Taxol, which adresses the same target Bcl-2, but is not metabolized by the cytochrome 2C8. Procedure: start to search for the targets and the metabolizing cytochromes of Taxol in the associated categories. The resulting lists contain among others the target Bcl-2 as well as the P450 cytochrome 2C8. Second, forward 2C8 and Bcl-2 into the query term box, combine them using the ‘NOT’ operator and submit the query. The resulting drug list contains two alternative drug candidates for Taxol (Docetaxel and Flupirtine).

Mentions: The integration of drug related information provides numerous different query entry points as well as global surveys on complex topics using heterogeneous data types (for an illustration of query capabilities see Figure 2).Figure 2.


SuperTarget and Matador: resources for exploring drug-target relationships.

Günther S, Kuhn M, Dunkel M, Campillos M, Senger C, Petsalaki E, Ahmed J, Urdiales EG, Gewiess A, Jensen LJ, Schneider R, Skoblo R, Russell RB, Bourne PE, Bork P, Preissner R - Nucleic Acids Res. (2007)

Example of a complex query: search for an alternative drug to Taxol, which adresses the same target Bcl-2, but is not metabolized by the cytochrome 2C8. Procedure: start to search for the targets and the metabolizing cytochromes of Taxol in the associated categories. The resulting lists contain among others the target Bcl-2 as well as the P450 cytochrome 2C8. Second, forward 2C8 and Bcl-2 into the query term box, combine them using the ‘NOT’ operator and submit the query. The resulting drug list contains two alternative drug candidates for Taxol (Docetaxel and Flupirtine).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238858&req=5

Figure 2: Example of a complex query: search for an alternative drug to Taxol, which adresses the same target Bcl-2, but is not metabolized by the cytochrome 2C8. Procedure: start to search for the targets and the metabolizing cytochromes of Taxol in the associated categories. The resulting lists contain among others the target Bcl-2 as well as the P450 cytochrome 2C8. Second, forward 2C8 and Bcl-2 into the query term box, combine them using the ‘NOT’ operator and submit the query. The resulting drug list contains two alternative drug candidates for Taxol (Docetaxel and Flupirtine).
Mentions: The integration of drug related information provides numerous different query entry points as well as global surveys on complex topics using heterogeneous data types (for an illustration of query capabilities see Figure 2).Figure 2.

Bottom Line: Therefore, we developed a one-stop data warehouse, SuperTarget that integrates drug-related information about medical indication areas, adverse drug effects, drug metabolization, pathways and Gene Ontology terms of the target proteins.The database contains more than 2500 target proteins, which are annotated with about 7300 relations to 1500 drugs; the vast majority of entries have pointers to the respective literature source.A subset of these drugs has been annotated with additional binding information and indirect interactions and is available as a separate resource called Matador.

View Article: PubMed Central - PubMed

Affiliation: Structural Bioinformatics Group, Institute of Molecular Biology and Bioinformatics, Charité-University Medicine Berlin, Arnimallee 22, 14195 Berlin, Germany.

ABSTRACT
The molecular basis of drug action is often not well understood. This is partly because the very abundant and diverse information generated in the past decades on drugs is hidden in millions of medical articles or textbooks. Therefore, we developed a one-stop data warehouse, SuperTarget that integrates drug-related information about medical indication areas, adverse drug effects, drug metabolization, pathways and Gene Ontology terms of the target proteins. An easy-to-use query interface enables the user to pose complex queries, for example to find drugs that target a certain pathway, interacting drugs that are metabolized by the same cytochrome P450 or drugs that target the same protein but are metabolized by different enzymes. Furthermore, we provide tools for 2D drug screening and sequence comparison of the targets. The database contains more than 2500 target proteins, which are annotated with about 7300 relations to 1500 drugs; the vast majority of entries have pointers to the respective literature source. A subset of these drugs has been annotated with additional binding information and indirect interactions and is available as a separate resource called Matador. SuperTarget and Matador are available at http://insilico.charite.de/supertarget and http://matador.embl.de.

Show MeSH
Related in: MedlinePlus