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WebMolCS: A Web-Based Interface for Visualizing Molecules in Three-Dimensional Chemical Spaces

Type of publication Peer-reviewed
Publikationsform Original article (peer-reviewed)
Author Awale Mahendra, Probst Daniel, Reymond Jean-Louis,
Project Exploiting and Extending GDB for Drug Discovery
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Original article (peer-reviewed)

Journal JCIM Journal of Chemical Information and Modeling
Volume (Issue) 57(4)
Page(s) 643 - 649
Title of proceedings JCIM Journal of Chemical Information and Modeling
DOI 10.1021/acs.jcim.6b00690

Open Access

Type of Open Access Publisher (Gold Open Access)


The concept of chemical space provides a convenient framework to analyze large collections of molecules by placing them in property spaces where distances represent similarities. Here we report webMolCS, a new type of web-based interface visualizing up to 5000 user-defined molecules in six different three-dimensional (3D) chemical spaces obtained by principal component analysis or similarity mapping of multidimensional property spaces describing composition (MQN: 42D molecular quantum numbers, SMIfp: 34D SMILES fingerprint), shapes and pharmacophores (APfp: 20D atom pair fingerprint, Xfp: 55D category extended atom pair fingerprint), and substructures (Sfp: 1024D binary substructure fingerprint, ECfp4:1024D extended connectivity fingerprint). Each molecule is shown as a sphere, and its structure appears on mouse over. The sphere is color-coded by similarity to the first compound in the list, by the list rank, or by a user-defined value, which reveals the relationship between any property encoded by these values and structural similarities. WebMolCS is freely available at