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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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Related in: MedlinePlus

System architecture and number of database entries of SuperTarget. The database contains the complete Uniprot with more than 3 million entries. Beside the targets, drugs and pathways the database provides 23 000 different GO-terms and 30 000 links to protein structures.
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Figure 1: System architecture and number of database entries of SuperTarget. The database contains the complete Uniprot with more than 3 million entries. Beside the targets, drugs and pathways the database provides 23 000 different GO-terms and 30 000 links to protein structures.

Mentions: To be able to obtain more information on the drug-target relations, SuperTarget provides links to physicochemical properties and further structural information of drugs. Proven or potential target proteins are represented by sequences as stored in UniProt (12), by functional annotations extracted from GOA (13) and by related pathway information provided by KEGG (9) (compare Figure 1). Adverse drug reactions were extracted from the free accessible Canadian Adverse Reaction Monitoring Program (CADRMP, http://www.hc-sc.gc.ca/).Figure 1.


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)

System architecture and number of database entries of SuperTarget. The database contains the complete Uniprot with more than 3 million entries. Beside the targets, drugs and pathways the database provides 23 000 different GO-terms and 30 000 links to protein structures.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 1: System architecture and number of database entries of SuperTarget. The database contains the complete Uniprot with more than 3 million entries. Beside the targets, drugs and pathways the database provides 23 000 different GO-terms and 30 000 links to protein structures.
Mentions: To be able to obtain more information on the drug-target relations, SuperTarget provides links to physicochemical properties and further structural information of drugs. Proven or potential target proteins are represented by sequences as stored in UniProt (12), by functional annotations extracted from GOA (13) and by related pathway information provided by KEGG (9) (compare Figure 1). Adverse drug reactions were extracted from the free accessible Canadian Adverse Reaction Monitoring Program (CADRMP, http://www.hc-sc.gc.ca/).Figure 1.

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