Connecting proteins with drug-like compounds: Open source drug discovery workflows with BindingDB and KNIME.
Database (Oxford)
; 20152015.
Article
in En
| MEDLINE
| ID: mdl-26384374
ABSTRACT
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.
Full text:
1
Collection:
01-internacional
Database:
MEDLINE
Main subject:
Pharmacokinetics
/
Pharmaceutical Preparations
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Proteins
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Drug Interactions
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Knowledge Bases
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Drug Discovery
Limits:
Animals
/
Humans
Language:
En
Journal:
Database (Oxford)
Year:
2015
Document type:
Article