Web-based 3D-visualization of the DrugBank chemical space

Awale, Mahendra; Reymond, Jean-Louis (2016). Web-based 3D-visualization of the DrugBank chemical space. Journal of cheminformatics, 8, p. 25. Springer 10.1186/s13321-016-0138-2

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BACKGROUND Similarly to the periodic table for elements, chemical space offers an organizing principle for representing the diversity of organic molecules, usually in the form of multi-dimensional property spaces that are subjected to dimensionality reduction methods to obtain 3D-spaces or 2D-maps suitable for visual inspection. Unfortunately, tools to look at chemical space on the internet are currently very limited. RESULTS Herein we present webDrugCS, a web application freely available at www.gdb.unibe.ch to visualize DrugBank (www.drugbank.ca, containing over 6000 investigational and approved drugs) in five different property spaces. WebDrugCS displays 3D-clouds of color-coded grid points representing molecules, whose structural formula is displayed on mouse over with an option to link to the corresponding molecule page at the DrugBank website. The 3D-clouds are obtained by principal component analysis of high dimensional property spaces describing constitution and topology (42D molecular quantum numbers MQN), structural features (34D SMILES fingerprint SMIfp), molecular shape (20D atom pair fingerprint APfp), pharmacophores (55D atom category extended atom pair fingerprint Xfp) and substructures (1024D binary substructure fingerprint Sfp). User defined molecules can be uploaded as SMILES lists and displayed together with DrugBank. In contrast to 2D-maps where many compounds fold onto each other, these 3D-spaces have a comparable resolution to their parent high-dimensional chemical space. CONCLUSION To the best of our knowledge webDrugCS is the first publicly available web tool for interactive visualization and exploration of the DrugBank chemical space in 3D. WebDrugCS works on computers, tablets and phones, and facilitates the visual exploration of DrugBank to rapidly learn about the structural diversity of small molecule drugs.Graphical abstractwebDrugCS visualization of DrugBank projected in 3D MQN space color-coded by ring count, with pointer showing the drug 5-fluorouracil.

Item Type:

Journal Article (Original Article)


08 Faculty of Science > Departement of Chemistry and Biochemistry
04 Faculty of Medicine > Other Institutions > NCCR TransCure

UniBE Contributor:

Awale, Mahendra and Reymond, Jean-Louis


500 Science > 570 Life sciences; biology
500 Science > 540 Chemistry








Valentina Rossetti

Date Deposited:

15 Sep 2016 11:20

Last Modified:

04 Feb 2019 18:07

Publisher DOI:


PubMed ID:


Uncontrolled Keywords:

Chemical space; DrugBank; Fingerprints; Molecular shape; Pharmacophores; Visualization





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