↓ Skip to main content

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

Overview of attention for article published in Journal of Cheminformatics, May 2016
Altmetric Badge

About this Attention Score

  • Good Attention Score compared to outputs of the same age (69th percentile)
  • Average Attention Score compared to outputs of the same age and source

Mentioned by

twitter
6 X users

Citations

dimensions_citation
14 Dimensions

Readers on

mendeley
59 Mendeley
You are seeing a free-to-access but limited selection of the activity Altmetric has collected about this research output. Click here to find out more.
Title
Web-based 3D-visualization of the DrugBank chemical space
Published in
Journal of Cheminformatics, May 2016
DOI 10.1186/s13321-016-0138-2
Pubmed ID
Authors

Mahendra Awale, Jean-Louis Reymond

Abstract

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. 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. 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.

X Demographics

X Demographics

The data shown below were collected from the profiles of 6 X users who shared this research output. Click here to find out more about how the information was compiled.
Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 59 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United Kingdom 1 2%
India 1 2%
Unknown 57 97%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 10 17%
Researcher 9 15%
Student > Bachelor 8 14%
Professor 7 12%
Student > Master 5 8%
Other 10 17%
Unknown 10 17%
Readers by discipline Count As %
Chemistry 24 41%
Pharmacology, Toxicology and Pharmaceutical Science 10 17%
Computer Science 4 7%
Medicine and Dentistry 3 5%
Biochemistry, Genetics and Molecular Biology 2 3%
Other 5 8%
Unknown 11 19%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 5. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 06 May 2016.
All research outputs
#6,302,737
of 22,867,327 outputs
Outputs from Journal of Cheminformatics
#530
of 837 outputs
Outputs of similar age
#89,482
of 298,972 outputs
Outputs of similar age from Journal of Cheminformatics
#8
of 14 outputs
Altmetric has tracked 22,867,327 research outputs across all sources so far. This one has received more attention than most of these and is in the 72nd percentile.
So far Altmetric has tracked 837 research outputs from this source. They typically receive a lot more attention than average, with a mean Attention Score of 10.9. This one is in the 36th percentile – i.e., 36% of its peers scored the same or lower than it.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 298,972 tracked outputs that were published within six weeks on either side of this one in any source. This one has gotten more attention than average, scoring higher than 69% of its contemporaries.
We're also able to compare this research output to 14 others from the same source and published within six weeks on either side of this one. This one is in the 42nd percentile – i.e., 42% of its contemporaries scored the same or lower than it.