Abstract
BackgroundSimilarly 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.ResultsHerein 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.ConclusionTo 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.
Highlights
To the periodic table for elements, chemical space offers an organizing principle for represent‐ ing 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
The concept of chemical space, whereby molecules are annotated with a set of quantitative molecular properties and placed in a high-dimensional property space with each dimension corresponding to a different property, offers a practical approach to represent the structural diversity of large molecule collections [1–28]
principal component analysis (PCA) of multidimensional property spaces In a multidimensional property space dimensions and the position of any molecule are defined by a set of molecular descriptors
Summary
To the periodic table for elements, chemical space offers an organizing principle for represent‐ ing 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. The concept of chemical space, whereby molecules are annotated with a set of quantitative molecular properties and placed in a high-dimensional property space with each dimension corresponding to a different property, offers a practical approach to represent the structural diversity of large molecule collections [1–28] Such high-dimensional spaces cannot be visualized directly but can be subjected to various dimensionality reduction methods to obtain. To make chemical space easier to inspect, we recently reported an interactive Java Applet representing databases of molecules as color-coded maps produced by projection of high-dimensional property spaces, defined by various molecular fingerprints, into two dimensions [32–37] In these so-called Mapplets the computer screen shows a color-coded 2D-image where each pixel contains one or several molecules projected at that point. The average molecule contained in each pixel is displayed on a sidewindow on mouse over, with an option to open the complete list of molecules in the pixel in a secondary window, and subsequently to link selected molecules to the database entry, or to perform similarity searches in the parent
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