Connecting proteins with drug-like compounds: Open source drug discovery workflows with BindingDB and KNIME.
Database (Oxford)
; 20152015.
Article
em 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.
Texto completo:
1
Base de dados:
MEDLINE
Assunto principal:
Farmacocinética
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Preparações Farmacêuticas
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Proteínas
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Interações Medicamentosas
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Bases de Conhecimento
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Descoberta de Drogas
Limite:
Animals
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Humans
Idioma:
En
Ano de publicação:
2015
Tipo de documento:
Article