WebMolCS: A Web-Based Interface for Visualizing Molecules in Three-Dimensional Chemical Spaces.
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 www.gdb.unibe.ch .
Department of Chemistry and Biochemistry, National Center of Competence in Research NCCR TransCure, University of Berne , Freiestrasse 3, 3012 Berne, Switzerland.
Mahendra
M
Awale
Department of Chemistry and Biochemistry, National Center of Competence in Research NCCR TransCure, University of Berne , Freiestrasse 3, 3012 Berne, Switzerland.
Daniel
D
Probst
Department of Chemistry and Biochemistry, National Center of Competence in Research NCCR TransCure, University of Berne , Freiestrasse 3, 3012 Berne, Switzerland.
Jean-Louis
0000-0003-2724-2942
JL
Reymond
D020407:Internet; D008958:Models, Molecular; D008968:Molecular Conformation; D014584:User-Computer Interface