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Connecting proteins with drug-like compounds: Open source drug discovery
workflows with BindingDB and KNIME
#MMPMID26384374
Nicola G
; Berthold MR
; Hedrick MP
; Gilson MK
Database (Oxford)
2015[]; 2015
(?): ? PMID26384374
show ga
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. Database
URL: www.bindingdb.org.
free
free
free
