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Connecting proteins with drug-like compounds : Open source drug discovery workflows with BindingDB and KNIME

Connecting proteins with drug-like compounds : Open source drug discovery workflows with BindingDB and KNIME

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NICOLA, George, Michael R. BERTHOLD, Michael P. HEDRICK, Michael K. GILSON, 2015. Connecting proteins with drug-like compounds : Open source drug discovery workflows with BindingDB and KNIME. In: Database: The Journal of Biological Databases and Curation. 2015, bav087. eISSN 1758-0463

@article{Nicola2015-09-16Conne-33315, title={Connecting proteins with drug-like compounds : Open source drug discovery workflows with BindingDB and KNIME}, year={2015}, doi={10.1093/database/bav087}, volume={2015}, journal={Database: The Journal of Biological Databases and Curation}, author={Nicola, George and Berthold, Michael R. and Hedrick, Michael P. and Gilson, Michael K.}, note={Article Number: bav087} }

<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bibo="http://purl.org/ontology/bibo/" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" > <rdf:Description rdf:about="https://kops.uni-konstanz.de/rdf/resource/123456789/33315"> <dc:creator>Gilson, Michael K.</dc:creator> <dcterms:available rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2016-03-14T15:33:52Z</dcterms:available> <dc:creator>Berthold, Michael R.</dc:creator> <dcterms:rights rdf:resource="http://nbn-resolving.de/urn:nbn:de:bsz:352-20150914100631302-4485392-8"/> <dc:contributor>Nicola, George</dc:contributor> <dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2016-03-14T15:33:52Z</dc:date> <bibo:uri rdf:resource="https://kops.uni-konstanz.de/handle/123456789/33315"/> <dc:language>eng</dc:language> <dcterms:title>Connecting proteins with drug-like compounds : Open source drug discovery workflows with BindingDB and KNIME</dcterms:title> <dc:contributor>Hedrick, Michael P.</dc:contributor> <dcterms:issued>2015-09-16</dcterms:issued> <dc:contributor>Gilson, Michael K.</dc:contributor> <dc:creator>Hedrick, Michael P.</dc:creator> <dcterms:abstract xml:lang="eng">Today's large, public databases of protein-small molecule interaction data are creating important new opportunities for data mining and integration. At the same time, new graphical user interface-based workflow tools offer facile alternatives to custom scripting for informatics and data analysis. Here, we illustrate how the large protein-ligand database BindingDB may be incorporated into KNIME workflows as a step toward the integration of pharmacological data with broader biomolecular analyses. Thus, we describe a collection of KNIME workflows that access BindingDB data via RESTful webservices and, for more intensive queries, via a local distillation of the full BindingDB dataset. We focus in particular on the KNIME implementation of knowledge-based tools to generate informed hypotheses regarding protein targets of bioactive compounds, based on notions of chemical similarity. A number of variants of this basic approach are tested for seven existing drugs with relatively ill-defined therapeutic targets, leading to replication of some previously confirmed results and discovery of new, high-quality hits. Implications for future development are discussed.</dcterms:abstract> <dc:creator>Nicola, George</dc:creator> <dc:contributor>Berthold, Michael R.</dc:contributor> </rdf:Description> </rdf:RDF>

Dateiabrufe seit 14.03.2016 (Informationen über die Zugriffsstatistik)

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