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Easily navigating chemical space has become more important due to the increasing size and diversity of publicly-accessible databases such as DrugBank, ChEMBL, or DSSTox, and associated high-throughput screening (HTS) and other datasets. Modelers typically rely on complex projection techniques using molecular descriptors computed for all the chemicals to be visualized. However, the multiple cheminformatics steps required to prepare, characterize, compute and explore those molecules, are technical, typically necessitate scripting skills, and thus represent a real obstacle for non-specialists. Inspired by the popular Google Maps application, we developed the ChemMaps.com webserver to easily navigate chemical spaces.
The first version of ChemMaps.com was developed to browse and visualize the space of 2,000 FDA-approved drugs and over 6,000 drug candidates based on the DrugBank database (https://www.drugbank.ca/) and was extended on ~47,000 environmental chemicals. In this new version, the chemical coverage has been extended to include the full DSSTox inventory (>700,000 chemicals and additional browsing, searching, and exporting/importing options were updated and developed. Users can now upload their own set of chemicals and visualize them on the available maps and/or define a new map from them. All computed data, e.g. coordinates, chemical descriptors, etc. can now be downloaded. Different navigation options have been also developed, including a distance computing on the fly for two selected chemicals and a faster and more responsive environment.). Users can search for specific compounds, overlay regulatory classification and labeling based on animal toxicity data, explore and export nearest neighbor space, refine the projections based on physicochemical properties, and link out to the EPA’s CompTox Dashboard (https://comptox.epa.gov/dashboard) for detailed information on a chemical. Work is ongoing to embed ChemMaps.com on the EPA’s CompTox Dashboard to provide real-time chemical space visualization specific to the compound of interest.
Borrel,A. et al. (2018) Exploring drug space with ChemMaps.com. Bioinformatics, 1–3.