DeCAF—Discrimination, Comparison, Alignment Tool for 2D PHarmacophores
AbstractComparison of small molecules is a common component of many cheminformatics workflows, including the design of new compounds and libraries as well as side-effect predictions and drug repurposing. Currently, large-scale comparison methods rely mostly on simple fingerprint representation of molecules, which take into account the structural similarities of compounds. Methods that utilize 3D information depend on multiple conformer generation steps, which are computationally expensive and can greatly influence their results. The aim of this study was to augment molecule representation with spatial and physicochemical properties while simultaneously avoiding conformer generation. To achieve this goal, we describe a molecule as an undirected graph in which the nodes correspond to atoms with pharmacophoric properties and the edges of the graph represent the distances between features. This approach combines the benefits of a conformation-free representation of a molecule with additional spatial information. We implemented our approach as an open-source Python module called DeCAF (Discrimination, Comparison, Alignment tool for 2D PHarmacophores), freely available at http://bitbucket.org/marta-sd/decaf. We show DeCAF’s strengths and weaknesses with usage examples and thorough statistical evaluation. Additionally, we show that our method can be manually tweaked to further improve the results for specific tasks. The full dataset on which DeCAF was evaluated and all scripts used to calculate and analyze the results are also provided. View Full-Text
- Supplementary File 1:
Supplementary (ZIP, 560 KB)
Scifeed alert for new publicationsNever miss any articles matching your research from any publisher
- Get alerts for new papers matching your research
- Find out the new papers from selected authors
- Updated daily for 49'000+ journals and 6000+ publishers
- Define your Scifeed now
Stepniewska-Dziubinska, M.M.; Zielenkiewicz, P.; Siedlecki, P. DeCAF—Discrimination, Comparison, Alignment Tool for 2D PHarmacophores. Molecules 2017, 22, 1128.
Stepniewska-Dziubinska MM, Zielenkiewicz P, Siedlecki P. DeCAF—Discrimination, Comparison, Alignment Tool for 2D PHarmacophores. Molecules. 2017; 22(7):1128.Chicago/Turabian Style
Stepniewska-Dziubinska, Marta M.; Zielenkiewicz, Piotr; Siedlecki, Pawel. 2017. "DeCAF—Discrimination, Comparison, Alignment Tool for 2D PHarmacophores." Molecules 22, no. 7: 1128.
Note that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. See further details here.