ArticleDatabase : the journal of biological databases and curation2015
Connecting proteins with drug-like compounds: Open source drug discovery workflows with BindingDB and KNIME.
Article in Database : the journal of biological databases and curation, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- The nitrovinyl moiety determines the cyto- and genotoxic profiles of β-nitrostyrene derivatives: evidence from in silico and in vitro evaluation.Archives of toxicology · 2026Article
- A comprehensive metabolome profiling of Terminalia chebula, Terminalia bellerica, and Phyllanthus emblica to explore the medicinal potential of Triphala.Scientific reports · 2024Article
- Towards reproducible computational drug discovery.Journal of cheminformatics · 2020Review
- 3D-e-Chem: Structural Cheminformatics Workflows for Computer-Aided Drug Discovery.ChemMedChem · 2018Article
- The Bioactive Protein-Ligand Conformation of GluN2C-Selective Positive Allosteric Modulators Bound to the NMDA Receptor.Molecular pharmacology · 2018Article
- An automated framework for QSAR model building.Journal of cheminformatics · 2018Article
- Unrecognised Outbreak: Human parainfluenza virus infections in a pediatric oncology unit. A new diagnostic PCR and virus monitoring system may allow early detection of future outbreaks.Wellcome open research · 2018Article
- Identifying relationships between unrelated pharmaceutical target proteins on the basis of shared active compounds.Future science OA · 2017Article
- PTS: a pharmaceutical target seeker.Database : the journal of biological databases and curation · 2017Article
- Exploring Protein-Protein Interactions as Drug Targets for Anti-cancer Therapy with In Silico Workflows.Methods in molecular biology (Clifton, N.J.) · 2017Article
- Analysis of drug-endogenous human metabolite similarities in terms of their maximum common substructures.Journal of cheminformatics · 2017Article
- BindingDB in 2015: A public database for medicinal chemistry, computational chemistry and systems pharmacology.Nucleic acids research · 2016Article
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Authors and funding
4 authors.
Funding
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.
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