The paper WebMolCS: a Web-Based Interface for Visualizing Molecules in 3D Chemical Spaces has been accepted for publication in the Journal of Chemical Information and Modeling.

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 3D chemical spaces obtained by principal component analysis or similarity mapping of multi-dimensional 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 or by the list rank, which reveals the relationship between any property encoded by the list rank and structural similarities. WebMolCS is freely available at www.gdbtools.unibe.ch:8080/webMolCS.

Author(s): Mahendra Awale, Daniel Probst, and Jean-Louis Reymond